use strict;
use warnings;
my @files = qw(001.file.a 001.file.b 002.file.a 002.file.b);

my @sorted_files;

for (@files){
    if (m/^(\d+)\./){
        push @{$sorted_files[$1]}, $_;
    } else {
        die "File name with unknown format: '$_'\n";
    }
}

for my $bucket (0 .. $#sorted_files){
    print "Processing bucket $bucket\n";
    for (@{$sorted_files[$bucket]}){
        print "\tprocessing file $_\n";
    }
}
__END__
Processing bucket 0
Processing bucket 1
        processing file 001.file.a
        processing file 001.file.b
Processing bucket 2
        processing file 002.file.a
        processing file 002.file.b