use strict;
use warnings;
use List::Util qw( all );

...
# create and populate my @matrix as before
...

my @indices =
(
    [0, 4, 0], [0, 4, 1], [0, 4, 2],
    [1, 4, 0], [1, 4, 1], [1, 4, 2],
    [2, 4, 0], [2, 4, 1], [2, 4, 2],
    [4, 4, 0], [4, 4, 1], [4, 4, 2],    # A
    [5, 4, 0], [5, 4, 1], [5, 4, 2],
    [6, 4, 0], [6, 4, 1], [6, 4, 2],
    [4, 0, 0], [4, 0, 1], [4, 0, 2],
    [4, 1, 0], [4, 1, 1], [4, 1, 2],
    [4, 2, 0], [4, 2, 1], [4, 2, 2],
    [4, 4, 0], [4, 4, 1], [4, 4, 2],    # B
    [4, 5, 0], [4, 5, 1], [4, 5, 2],
    [4, 6, 0], [4, 6, 1], [4, 6, 2],
);

my   @to_test;
push @to_test, $matrix[ $_->[0] ][ $_->[1] ][ $_->[2] ] for @indices;

print "It worked\n" if all { $_ == 1 } @to_test;