Perhaps the following will be helpful:

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;
}
[download]

Output:

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

The subroutine sorts and then takes the top three largest 'minion' numbers to populate a hash, then greps through the 'master' array to allow only the three 'minion' arrays pass which contain one of those three top values.

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