use strict;
use warnings;
use Data::Dumper;

my @masterArray = (
	[ "this", "that", 12563,  "something", "else" ],
	[ "this", "that", 10,     "something", "else" ],
	[ "this", "that", 1,      "something", "else" ],
	[ "this", "that", 125638, "something", "else" ],
	[ "this", "that", 300000, "something", "else" ],
);

subDiscarder( \@masterArray );

print Dumper \@masterArray;

sub subDiscarder {
	my ($arrayRef) = @_;
	my %nums =
	  map $_ => 1,
	  ( sort { $b <=> $a } map $_->[2], @$arrayRef )[ 0 .. 2 ];
	@$arrayRef = grep exists $nums{ $_->[2] }, @$arrayRef;
}

##</code><code>##

$VAR1 = [
          [
            'this',
            'that',
            12563,
            'something',
            'else'
          ],
          [
            'this',
            'that',
            125638,
            'something',
            'else'
          ],
          [
            'this',
            'that',
            300000,
            'something',
            'else'
          ]
        ];