File::Copy's copy function copies files, not directories. You can use File::Find to find the files and use those as input to File::Copy.

use strict;
use warnings;
use File::Copy;
use File::Find;
my @fromdirs = qw (/tmp/foo);
my $todir    = q{/tmp/bar};

find(
  sub {
    if (-f) {
      print "$File::Find::name -> $todir";
      copy($File::Find::name, $todir)
        or die(q{copy failed:} . $!);
    }
  },
  @fromdirs
);

__END__
$ mkdir -p /tmp/foo
$ mkdir -p /tmp/bar
$ touch /tmp/foo/1
$ touch /tmp/foo/2
$ perl -l 635503.pl
/tmp/foo/1 -> /tmp/bar
/tmp/foo/2 -> /tmp/bar
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