Ok here we go: I don't know where the +'s are coming from but they are not in the code...the red pluses that is...

#!/usr/local/bin/perl


#+---------------------------------------------+
#|            Configuration Options            |
#+---------------------------------------------+


$dirname = "C:\\Working\\";
$mastertemp = "C:\\master.txt";
$dupefile = "C:\\dupes.txt";
$newmaster = "C:\\newmaster.txt";


main();


sub main{
    dirlist();
    extract_data();
    output_results();    
}


sub dirlist{                                                          
+  # Pull Directory Listing
    opendir(DIR, $dirname) or die "can't opendir $dirname: $!";       
+  # open the directory
   while (defined($file = readdir(DIR))) {                            
+  # read the directory
    next if $file =~ /^\.\.?$/;
            push(@dirlisting, $file);                                #
+ put dirlist in @dirlisting
    }
}

sub extract_data {                                                    
+  # Get list of archived files
%lines;
%dupez;
    foreach (@dirlisting){                                            
+  #
        $filename1 = $_;
    open(INPUTFILE, "$dirname" . "$filename1");
    open(MASTERTEMP, ">>$mastertemp");
    open(DUPES, ">>$dupefile");
    while (<INPUTFILE>) {
        $custID = substr($_,0,9);
        $ccn    = substr($_,22,16);
        $expy   = substr($_,44,4);
        $type   = substr($_,50,3);
        $amount = substr($_,58,6);
#        $amount =~ s/^\s+//;
        if (($custID lt 0) || ($custID eq "Name     ")){
        }else{
        dupeczech();
        print MASTERTEMP "$custID"."             "."$ccn"."      "."$e
+xpy"."  "."$type"."     "."$amount\n";
        }
        
    }
    close(INPUTFILE);
    close(MASTERTEMP);
    close(DUPES);
    }    
}
    

sub dupeczech {
    $lines{$ccn}++;        #add one to the value if it hasn't been def
+ined yet it sets it equal to 1
    if($lines{$ccn} == 2){ #been seen before so add to dupes list
    push @dupes, $ccn;
#    print "$ccn $custID $lines{$ccn}\n";
#    print DUPES "$custID"."             "."$ccn"."      "."$expy\n";
    }
}

sub output_results {
    open(MASTERTEMP, "$mastertemp");
    open(DUPES, ">>$dupefile");
    open(NEWMASTER, ">>$newmaster");
    while (<MASTERTEMP>) {
        $custID = substr($_,0,9);
        $ccn    = substr($_,22,16);
        $expy   = substr($_,44,4);
        $type   = substr($_,50,3);
        $amount = substr($_,58,6);
        
        foreach (@dupes){
        if ($ccn eq $_) {
            print DUPES "$custID"."             "."$ccn"."      "."$ex
+py"."  "."$type"."     "."$amount\n";
            $dupez{$ccn}++;
            
        }
        
        }
        if (!$dupez{$ccn}){
        print NEWMASTER "$custID"."             "."$ccn"."      "."$ex
+py"."  "."$type"."     "."$amount\n";
    }
        
    }
    
    close(NEWMASTER);
    close(MASTERTEMP);
    close(DUPES);

}
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