It strikes me that, assuming an invocation of perl <script> <target directory> <source directory>..., the following may be something along the lines you require (i.e. untested)...

use warnings;
use strict;

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

use autodie qw/File::Copy::copy/;

my $tgt_dir = shift;

find(
    sub {
        return unless -f $_;
        copy($File::Find::name, qq($tgt_dir/$_));
    },
    @ARGV
)
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