Have a look at Math::Combinatorics which will allow you to calculate all of the combinations. You can then do what you like with the results.

#! /usr/bin/perl
#
use strict;
use warnings;

use Math::Combinatorics;
my @files;
push @files, "file$_" foreach (1..36);

my $c = Math::Combinatorics->new( count => 3, data => \@files);
while (my @combo = $c->next_combination()) {
    my %combins;
    @combins{@combo}=();
    my @leftovers = grep {!exists($combins{$_})} @files;
    print "Choose: @combo\tLeave: @leftovers\n";}
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update: Obviously you would populate the @files array using a glob or similar. If your files aren't large you could pre-read them into memory.