%hash = { 
             filename1 => { id1 => 1, id2 => 1 },
             filename2 => { id1 => 3, id2 => 4 }
};

##</code><code>##

use strict;
use warnings;
#NOT TESTED

my %filehash;
for ($i=1; $i<=$number; $i++) {
    my $filename = "file$i";
    open (lookup, "<$filename") or die "Can't open $filename : $!\n";
         
    while (<lookup>) {
       ($ref_name, $ref_id) = (split /\t/, $_)[3,4];
       $filehash{$filename}{$ref_id} = $ref_name; 
    }
}