i borrowed the directory parsing part of the script from cdarke and modified it just a hair... so big thanks to that guy :)

Here is the full script, please help guide me as to what i may have done wrong, or if you download the script and files and figure out an alot faster or shorter version, please show me cz i baked my brain on this for a day and a half(tho i do feel like i am getting somewhat better lol)

use strict;
use warnings;
use File::Slurp;
use File::Copy qw(copy);
use File::Path qw(make_path);

my @dev_flash000 = ();
my @dev_flash001 = ();
my @dev_flash002 = ();
my @dev_flash003 = ();
my @dev_flash004 = ();
my @dev_flash005 = ();
my @dev_flash006 = ();
my @dev_flash007 = ();
my @dev_flash008 = ();
my @dev_flash009 = ();
my @dev_flash010 = ();
my @dev_flash011 = ();
my @dev_flash012 = ();
my @dev_flash013 = ();
my @dev_flash014 = ();
my @dev_flash015 = ();
my @dev_flash016 = ();
my @dev_flash017 = ();
my @dev_flash018 = ();
my @dev_flash019 = ();
my @dev_flash020 = ();
my @dev_flash021 = ();
my @dev_flash022 = ();
my @dev_flash023 = ();
my @dev_flash024 = ();
my @dev_flash025 = ();
my @dev_flash026 = ();
my @dev_flash027 = ();


sub make_folders {
    my $tempdir = "temp";
    opendir( DIR, $tempdir );

    while ( my $tempfile = readdir(DIR) ) {
        next if -d $tempfile;
        make_path("copied_files/$tempfile/duplicate");
    }
}

sub search_dir {
    my ($dir) = @_;

    my $dh;
    if ( !opendir( $dh, $dir ) ) {

        return;
    }

    while ( my $file = readdir($dh) ) {

        next if -d $file;
        my $path = "$dir/$file";
        if ( -d $path ) {
            search_dir($path);
        }
        else {

            extract_files( $dir, $file );
        }
    }

}

sub extract_files {
    my $des = '';

    my ( $dir, $file ) = @_;

    my $dev_flash000 = read_file('temp/dev_flash000');
    my $dev_flash001 = read_file('temp/dev_flash001');
    my $dev_flash002 = read_file('temp/dev_flash002');
    my $dev_flash003 = read_file('temp/dev_flash003');
    my $dev_flash004 = read_file('temp/dev_flash004');
    my $dev_flash005 = read_file('temp/dev_flash005');
    my $dev_flash006 = read_file('temp/dev_flash006');
    my $dev_flash007 = read_file('temp/dev_flash007');
    my $dev_flash008 = read_file('temp/dev_flash008');
    my $dev_flash009 = read_file('temp/dev_flash009');
    my $dev_flash010 = read_file('temp/dev_flash010');
    my $dev_flash011 = read_file('temp/dev_flash011');
    my $dev_flash012 = read_file('temp/dev_flash012');
    my $dev_flash013 = read_file('temp/dev_flash013');
    my $dev_flash014 = read_file('temp/dev_flash014');
    my $dev_flash015 = read_file('temp/dev_flash015');
    my $dev_flash016 = read_file('temp/dev_flash016');
    my $dev_flash017 = read_file('temp/dev_flash017');
    my $dev_flash018 = read_file('temp/dev_flash018');
    my $dev_flash019 = read_file('temp/dev_flash019');
    my $dev_flash020 = read_file('temp/dev_flash020');
    my $dev_flash021 = read_file('temp/dev_flash021');
    my $dev_flash022 = read_file('temp/dev_flash022');
    my $dev_flash023 = read_file('temp/dev_flash023');
    my $dev_flash024 = read_file('temp/dev_flash024');
    my $dev_flash025 = read_file('temp/dev_flash025');
    my $dev_flash026 = read_file('temp/dev_flash026');
    my $dev_flash027 = read_file('temp/dev_flash027');

    if ( $dev_flash000 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash000/$file" ) {
            push @dev_flash000, "$file\n";
            my $des = "copied_files/dev_flash000/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash000, "$file\n";
            my $des = "copied_files/dev_flash000/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash001 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash001/$file" ) {
            push @dev_flash001, "$file\n";
            my $des = "copied_files/dev_flash001/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash001, "$file\n";
            my $des = "copied_files/dev_flash001/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash002 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash002/$file" ) {
            push @dev_flash002, "$file\n";
            my $des = "copied_files/dev_flash002/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash002, "$file\n";
            my $des = "copied_files/dev_flash002/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash003 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash003/$file" ) {
            push @dev_flash003, "$file\n";
            my $des = "copied_files/dev_flash003/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash003, "$file\n";
            my $des = "copied_files/dev_flash003/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash004 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash004/$file" ) {
            push @dev_flash004, "$file\n";
            my $des = "copied_files/dev_flash004/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash004, "$file\n";
            my $des = "copied_files/dev_flash004/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash005 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash005/$file" ) {
            push @dev_flash005, "$file\n";
            my $des = "copied_files/dev_flash005/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash005, "$file\n";
            my $des = "copied_files/dev_flash005/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash006 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash006/$file" ) {
            push @dev_flash006, "$file\n";
            my $des = "copied_files/dev_flash006/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash006, "$file\n";
            my $des = "copied_files/dev_flash006/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash007 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash007/$file" ) {
            push @dev_flash007, "$file\n";
            my $des = "copied_files/dev_flash007/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash007, "$file\n";
            my $des = "copied_files/dev_flash007/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash008 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash008/$file" ) {
            push @dev_flash008, "$file\n";
            my $des = "copied_files/dev_flash008/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash008, "$file\n";
            my $des = "copied_files/dev_flash008/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash009 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash009/$file" ) {
            push @dev_flash009, "$file\n";
            my $des = "copied_files/dev_flash009/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash009, "$file\n";
            my $des = "copied_files/dev_flash009/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash010 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash010/$file" ) {
            push @dev_flash010, "$file\n";
            my $des = "copied_files/dev_flash010/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash010, "$file\n";
            my $des = "copied_files/dev_flash010/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash011 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash011/$file" ) {
            push @dev_flash011, "$file\n";
            my $des = "copied_files/dev_flash011/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash011, "$file\n";
            my $des = "copied_files/dev_flash011/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash012 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash012/$file" ) {
            push @dev_flash012, "$file\n";
            my $des = "copied_files/dev_flash012/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash012, "$file\n";
            my $des = "copied_files/dev_flash012/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash013 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash013/$file" ) {
            push @dev_flash013, "$file\n";
            my $des = "copied_files/dev_flash013/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash013, "$file\n";
            my $des = "copied_files/dev_flash013/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash014 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash014/$file" ) {
            push @dev_flash014, "$file\n";
            my $des = "copied_files/dev_flash014/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash014, "$file\n";
            my $des = "copied_files/dev_flash014/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash015 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash015/$file" ) {
            push @dev_flash015, "$file\n";
            my $des = "copied_files/dev_flash015/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash015, "$file\n";
            my $des = "copied_files/dev_flash015/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash016 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash016/$file" ) {
            push @dev_flash016, "$file\n";
            my $des = "copied_files/dev_flash016/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash016, "$file\n";
            my $des = "copied_files/dev_flash016/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash017 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash017/$file" ) {
            push @dev_flash017, "$file\n";
            my $des = "copied_files/dev_flash017/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash017, "$file\n";
            my $des = "copied_files/dev_flash017/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash018 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash018/$file" ) {
            push @dev_flash018, "$file\n";
            my $des = "copied_files/dev_flash018/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash018, "$file\n";
            my $des = "copied_files/dev_flash018/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash019 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash019/$file" ) {
            push @dev_flash019, "$file\n";
            my $des = "copied_files/dev_flash019/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash019, "$file\n";
            my $des = "copied_files/dev_flash019/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash020 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash020/$file" ) {
            push @dev_flash020, "$file\n";
            my $des = "copied_files/dev_flash020/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash020, "$file\n";
            my $des = "copied_files/dev_flash020/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash021 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash021/$file" ) {
            push @dev_flash021, "$file\n";
            my $des = "copied_files/dev_flash021/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash021, "$file\n";
            my $des = "copied_files/dev_flash021/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash022 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash022/$file" ) {
            push @dev_flash022, "$file\n";
            my $des = "copied_files/dev_flash022/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash022, "$file\n";
            my $des = "copied_files/dev_flash022/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash023 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash023/$file" ) {
            push @dev_flash023, "$file\n";
            my $des = "copied_files/dev_flash023/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash023, "$file\n";
            my $des = "copied_files/dev_flash023/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash024 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash024/$file" ) {
            push @dev_flash024, "$file\n";
            my $des = "copied_files/dev_flash024/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash024, "$file\n";
            my $des = "copied_files/dev_flash024/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash025 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash025/$file" ) {
            push @dev_flash025, "$file\n";
            my $des = "copied_files/dev_flash025/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash025, "$file\n";
            my $des = "copied_files/dev_flash025/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash026 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash026/$file" ) {
            push @dev_flash026, "$file\n";
            my $des = "copied_files/dev_flash026/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash026, "$file\n";
            my $des = "copied_files/dev_flash026/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    elsif ( $dev_flash027 =~ /\b$file\b/i ) {
        if ( -e "copied_files/dev_flash027/$file" ) {
            push @dev_flash027, "$file\n";
            my $des = "copied_files/dev_flash027/duplicate/";
            copy( "$dir/$file", $des ) or die "$!";
        }
        else {
            push @dev_flash027, "$file\n";
            my $des = "copied_files/dev_flash027/";
            copy( "$dir/$file", $des ) or die "$!";
        }
    }
    else {
###do nothing

    }

}

sub print_dev_flash {

    if (@dev_flash000 == 0){
    print '';
    }else{
    print "\n\n    dev_flash000\n|==================================>\
+n";
    foreach my $filename(@dev_flash000){
    print "\t$filename";
    }
    }

    if (@dev_flash001 == 0){
    print '';
    }else{
    print "\n\n    dev_flash001\n|==================================>\
+n";
    foreach my $filename(@dev_flash001){
    print "\t$filename";
    }
    }

    if (@dev_flash002 == 0){
    print '';
    }else{
    print "\n\n    dev_flash002\n|==================================>\
+n";
    foreach my $filename(@dev_flash002){
    print "\t$filename";
    }
    }

    if (@dev_flash003 == 0){
    print '';
    }else{
    print "\n\n    dev_flash003\n|==================================>\
+n";
    foreach my $filename(@dev_flash003){
    print "\t$filename";
    }
    }

    if (@dev_flash004 == 0){
    print '';
    }else{
    print "\n\n    dev_flash004\n|==================================>\
+n";
    foreach my $filename(@dev_flash004){
    print "\t$filename";
    }
    }

    if (@dev_flash005 == 0){
    print '';
    }else{
    print "\n\n    dev_flash005\n|==================================>\
+n";
    foreach my $filename(@dev_flash005){
    print "\t$filename";
    }
    }

    if (@dev_flash006 == 0){
    print '';
    }else{
    print "\n\n    dev_flash006\n|==================================>\
+n";
    foreach my $filename(@dev_flash006){
    print "\t$filename";
    }
    }

    if (@dev_flash007 == 0){
    print '';
    }else{
    print "\n\n    dev_flash007\n|==================================>\
+n";
    foreach my $filename(@dev_flash007){
    print "\t$filename";
    }
    }

    if (@dev_flash008 == 0){
    print '';
    }else{
    print "\n\n    dev_flash008\n|==================================>\
+n";
    foreach my $filename(@dev_flash008){
    print "\t$filename";
    }
    }

    if (@dev_flash009 == 0){
    print '';
    }else{
    print "\n\n    dev_flash009\n|==================================>\
+n";
    foreach my $filename(@dev_flash009){
    print "\t$filename";
    }
    }

    if (@dev_flash010 == 0){
    print '';
    }else{
    print "\n\n    dev_flash010\n|==================================>\
+n";
    foreach my $filename(@dev_flash010){
    print "\t$filename";
    }
    }

    if (@dev_flash011 == 0){
    print '';
    }else{
    print "\n\n    dev_flash011\n|==================================>\
+n";
    foreach my $filename(@dev_flash011){
    print "\t$filename";
    }
    }

    if (@dev_flash012 == 0){
    print '';
    }else{
    print "\n\n    dev_flash012\n|==================================>\
+n";
    foreach my $filename(@dev_flash012){
    print "\t$filename";
    }
    }

    if (@dev_flash013 == 0){
    print '';
    }else{
    print "\n\n    dev_flash013\n|==================================>\
+n";
    foreach my $filename(@dev_flash013){
    print "\t$filename";
    }
    }

    if (@dev_flash014 == 0){
    print '';
    }else{
    print "\n\n    dev_flash014\n|==================================>\
+n";
    foreach my $filename(@dev_flash014){
    print "\t$filename";
    }
    }

    if (@dev_flash015 == 0){
    print '';
    }else{
    print "\n\n    dev_flash015\n|==================================>\
+n";
    foreach my $filename(@dev_flash015){
    print "\t$filename";
    }
    }

    if (@dev_flash016 == 0){
    print '';
    }else{
    print "\n\n    dev_flash016\n|==================================>\
+n";
    foreach my $filename(@dev_flash016){
    print "\t$filename";
    }
    }

    if (@dev_flash017 == 0){
    print '';
    }else{
    print "\n\n    dev_flash017\n|==================================>\
+n";
    foreach my $filename(@dev_flash017){
    print "\t$filename";
    }
    }

    if (@dev_flash018 == 0){
    print '';
    }else{
    print "\n\n    dev_flash018\n|==================================>\
+n";
    foreach my $filename(@dev_flash018){
    print "\t$filename";
    }
    }

    if (@dev_flash019 == 0){
    print '';
    }else{
    print "\n\n    dev_flash019\n|==================================>\
+n";
    foreach my $filename(@dev_flash019){
    print "\t$filename";
    }
    }

    if (@dev_flash020 == 0){
    print '';
    }else{
    print "\n\n    dev_flash020\n|==================================>\
+n";
    foreach my $filename(@dev_flash020){
    print "\t$filename";
    }
    }

    if (@dev_flash021 == 0){
    print '';
    }else{

    print "\n\n    dev_flash021\n|==================================>\
+n";
    foreach my $filename(@dev_flash021){
    print "\t$filename";
    }
    }

    if (@dev_flash022 == 0){
    print '';
    }else{
    print "\n\n    dev_flash022\n|==================================>\
+n";
    foreach my $filename(@dev_flash022){
    print "\t$filename";
    }
    }

    if (@dev_flash023 == 0){
    print '';
    }else{
    print "\n\n    dev_flash023\n|==================================>\
+n";
    foreach my $filename(@dev_flash023){
    print "\t$filename";
    }
    }

    if (@dev_flash024 == 0){
    print '';
    }else{
    print "\n\n    dev_flash024\n|==================================>\
+n";
    foreach my $filename(@dev_flash024){
    print "\t$filename";
    }
    }

    if (@dev_flash025 == 0){
    print '';
    }else{
    print "\n\n    dev_flash025\n|==================================>\
+n";
    foreach my $filename(@dev_flash025){
    print "\t$filename";
    }
    }

    if (@dev_flash026 == 0){
    print '';
    }else{
    print "\n\n    dev_flash026\n|==================================>\
+n";
    foreach my $filename(@dev_flash026){
    print "\t$filename";
    }
    }

    if (@dev_flash027 == 0){
    print '';
    }else{
    print "\n\n    dev_flash027\n|==================================>\
+n";
    foreach my $filename(@dev_flash027){
    print "\t$filename";
    }
    }

}

my $dir = $ARGV[0];
chomp($dir);
if ( not defined $dir ) {
    print "\nUsage: scan.pl dev_flash\n";
    exit(0);
}

make_folders();
search_dir($dir);
print_dev_flash();
[download]

What made this so hard for me was each file needed to go into a specific directory, thats where i got the idea to name the directory after the filenames in the temp folder ( if you download the files you will see what i mean ). i need to go back through and add my parenthesis around strings and variables, just to keep it clean ofcourse, but its working great on win7 64 bit with active state. But hopefully someone is able to crush these 700 something lines of code down some. i am proud of this and i even used warnings; and use strict; and no errors ;)

here are the files , just download them and unzip it anywhere and run the script. and you will see what it does.