#UNTESTED
use strict;
use warnings;
my %files = ( FOO => { A => 2 }, BAR => { B => 3 } );
MAIN: while (<FH>) {
    my ($col1, $col2) = split m/\s+/;
    foreach my $file (keys %files) {
        if (exists $files{$file}{$col2} ) {
            #do something;
            next MAIN;
        }
    }
}