You don't post your regular expression for us to take a look at it, but I think that you need to use the non greedy operator '?' in your re. Like:
#!/usr/bin/perl -wT
use strict;
my $s = 'stuff <% junk %> more stuff <% more junk %> end';
print "$s\n";
$s =~ s/<%.*?%>//g;
print "$s\n";
Which makes the re to take the shortest match.
HTH God bless you rruiz
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