Does the script really die because of that? I ran the following in one terminal:

my $list = join ',', 'a' .. 'z';
mkdir '1';
open my $FH, '>', $_ for glob '1/' . ("{$list}" x 3);
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And while it was running, I ran the following in the same directory in the second terminal:

use File::Path qw{ remove_tree };

print remove_tree('1');
print "FINISHED\n";
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I got the error message you mentioned, but "FINISHED" was printed, too, so the program didn't die. The documentation is somehow unclear on this:

If make_path or remove_tree encounter an error, a diagnostic message will be printed to STDERR via carp (for non-fatal errors), or via croak (for fatal errors).

If you just want to avoid the message, you can use the documented error option:

use Data::Dumper;
use File::Path qw{ remove_tree };

my $err;
remove_tree('1', { error => \$err });
print Dumper($err);
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Which returns:

 $VAR1 = [
          {
            '1' => 'cannot remove directory: Directory not empty'
          }
        ];
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