I get a values of 3

How do you do that? You should get a value of 2. viz:

$  cat mat.pl 
#!/usr/bin/perl -w

use strict;
use warnings;

my $value1 = 1;
my $value2 = 1;
my $value3 = 1;
my $value4 = 1;
my $value5 = 1;
my $value6 = 1;

my @myMatrix = ( [$value1,$value2,$value3],
                     [$value4,$value5,$value6]);
my $matrixSize = @myMatrix;

print $matrixSize . "\n";
$ perl mat.pl
2
$
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