So I was right. You _are_ trying to reinvent File::Find :)

I think you want something a bit like this (but I haven't had a chance to test it)

#!/use/bin/perl

use strict;
use warnings;

use File::Find;
use File::Path;
use File::Copy;

@_ >= 2 or die "Usage: $0 <source_dir> <dest_dir>\n";

my ($src, $dest) = @_;

find(\&do_this, $src);

sub do_this {
  if (-d) {
    mkpath([$File::Find::name]);
  } else {
    my $new = $File::Find::name;
    $new =~ s|/$src/|/$dest/|;
    copy $_, $new;
  }
}
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