Updated, I missed the multi-line part...added a s to my regexp
This actually ran? I would think the parser would have halted when it got to the </script> part...it should have ended the regex.

You probably want to try something like this:

#!/usr/bin/perl -wl

use strict;
use warnings;


my $test = "before script<script> stuff and more stuff \n stuff\nstuff
+\nstuff</script> after script";

$test =~ s%<script>(.*?)</script>%%gs;

print "Test is $test\n";
[download]

Which outputs:

./test.pl 
    Test is before script  after script
[download]

This uses a nifty trick, you can use (just about) anything for the start/end characters for a regexp/search-replace to avoid conflicts in the matching/replacing string. Here I have used the percent signs instead.

Have fun!