Obviously you probably done want to push the file into an array if they are large.

use strict;
use warnings;

use Data::Dumper;

my $file_base = '1.TXT';
my $file_filter = '2.TXT';

open ( FILTER, "<$file_filter" ) 
    or die "Die: Could not open $file_filter: $!";

open ( BASE, "<$file_base" )
    or die "Die: Could not open $file_base: $!";

my @filterArray = <FILTER>;
my @baseArray = <BASE>;
close BASE;
close FILTER;

unless( arrayDiff( \@filterArray , \@baseArray ) )
{
    print "Success!";
}

sub arrayDiff {
    my $array1 = shift(@_);
    my $array2 = shift(@_); 

    my %array1_hash;
    my %array2_hash;

    # Create a hash entry for each element in @array1
    for my $element ( @{$array1} ) {
       $array1_hash{$element} = @{$array1};
    }

    # Same for @array2: This time, use map instead of a loop
    map { $array2_hash{$_} = 1 } @{$array2};

    for my $entry ( @{$array2} ) {
        if ( not $array1_hash{$entry} ) {
            return 1;  #Entry in @array2 but not @array1: Differ
        }
    }
    if ( keys %array1_hash != keys %array2_hash ) {
       return 1;   #Arrays differ
    }
    else {
       return 0;   #Arrays contain the same elements
    }
}
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Monks>perl  1156663.pl
Success!
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