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my $element = $matrix[0]->[4]; 
# or by shorthand:
my $element2 = $matrix[0][4];

$matrix[6]->[3] = 8; # or the same shorthand as above

my @row6 = @{ $matrix[6] }; # to a list
my $listRef6 = $matrix[6]; # to a listreference

foreach my $row (@matrix) {
  print join ("\t", @$row);
}