Snapshot.pm is just a text file with a list of modules inside. Now, Perl happens to be a tool that was created with text manipulation in mind. Therefore, why don't you use it as a filter?

The quick way:

$ perl -i.bak -ne 'print unless /(?:Module1|Module2)/' Snapshot.pm
[download]

The classic way:

#filter_snapshot.pl
use strict;
use warnings;
my @exclude_modules = map {chomp;quotemeta($_)} <DATA>;

FILTER:
while (<>)
{
   for my $excluded (@exclude_modules)
   {
        next FILTER if /$excluded/
   }
   print ;
}

__DATA__
module1
Module2
Module3::SubModule
Module4
[download]

Invoke it as

$ perl filter_snapshot.pl Snapshot.pm > New_Snapshot.pm
[download]