Here's some fuel for thought:

#!/usr/bin/perl -w 
use strict;
use File::Copy;

do_copy("path/to/dir","path/to/dest");


exit(0);

sub do_copy {
    my ($src_path,$dest_path)=@_;

    opendir(DIR,$src_path) or die "$src_path: $!";
    while(my $entry=readdir(DIR)){
        next if $entry eq '..';
        next if $entry eq '.';
        my $sfqp = $src_path . "/" . $entry;
        my $dfqp = $dest_path . "/" . $entry;
        if ( -d $sfqp ) {
            mkdir $dfq,0755; # Change to your mask 
            do_copy($sfqp,$dfqp); # Recursion
        } elsif ( -f $sfqp ) { 
            copy $sfqp,$dfqp or die $!
        }
    }
}
[download]

Now, if you just want to move files ending in ".cmd" you'd add a line just before the copy call something like:

next unless $entry =~ m@\.cmd$@;
[download]

so it will ignore all but what you want.