Well, you've got a two-dimensional array, which in perl is a list () of references to lists [].
If you want to get the element 0/4, just write:

my $element = $matrix[0]->[4]; 
# or by shorthand:
my $element2 = $matrix[0][4];
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If you want to change the element 6/3 to 8, just write

$matrix[6]->[3] = 8; # or the same shorthand as above
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If you want go get the whole row number 6:

my @row6 = @{ $matrix[6] }; # to a list
my $listRef6 = $matrix[6]; # to a listreference
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If you want to print this array formatted, you could also do the following:

foreach my $row (@matrix) {
  print join ("\t", @$row);
}
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Further information gives you: perldoc perllol

Best regards,
perl -le "s==*F=e=>y~\*martinF~stronat~=>s~[^\w]~~g=>chop,print"