#!/usr/bin/perl -w
use strict;

my @array = qw(001.file.a 001.file.b 002.file.a 002.file.b);
my %hash;
for my $filename (@array){
    $filename =~ /^(\d+)/;
    push @{$hash{$1}}, $filename;
}

for my $group (sort { $a <=> $b } keys %hash){
    print "Processing group '$group':\n";
    for my $file (@{$hash{$group}}){
        print "\tProcessing $file:\n";

        ### Do stuff

    }
}