read next and last.
You should get code similar to this:

#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;
        }
    }
}
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Also please use strict; and use warnings; you'll save yourself a lot of grief.

UPDATE:

Although it might be even cleaner (clearer and more maintainable) by creating a sub.

##ALSO UNTESTED
while (<FH>) {
    my ($col1, $col2) = split m/\s+/;
    stuff_i_need_do($col1) if ( check_for_condition(\%files,$col2) );
}

sub check_for_condition {
    my $files = shift || return undef;
    my $col   = shift || return undef;
    foreach my $file ( keys %{$files} ) {
        return 1 if (exists $files{$file}{$col2} );
    }
    return undef;
}

sub stuff_i_need_to_do {
   my $stuff = shift;
   #do something;
}
[download]