Some more code would help. Currently I imagine your base module and main program to be something like this:

#!/usr/bin/perl -w
use strict;
use vars qw(%rules);

# From the base package
sub filter_names {
    my ($rule_name,@files) = @_;
    my $rule = $main::rules{ $rule_name };
    grep {/$rule/} @files
};

%rules = (
   INPUT_FILE_DESCRIPTION => "^Remote.*",
   OTHER_FILES => "^(?!Remote)"
);

my @files = <DATA>;
chomp @files;

for my $rule (qw(INPUT_FILE_DESCRIPTION OTHER_FILES)) {
    print "$rule\n";
    print "$_\n" for filter_names($rule, @files);
};
__DATA__
Remote1
Other1
Remote2
Other2
Remote3
Another
[download]

My solution uses the negative lookahead, anchored to the start of the string. See perlre to find out more about negative lookahead. Also, you might want to consider a different approach that remembers whether a file was handled by a rule already and then raising an error about all unhandled files. Doing that would be possible by remembering for each file the rule(s) that applied.