The mapat method on a matrix object could give you a way to flatten it into an array. The transpose method could return a transposed matrix object, or transpose the current object in-place. but the real power would come from something like this:

 #assume $m1 and $m2 are matrix objects

 my $m3 = $m1->ApplyFunction(\&mysub, $m2);

 ....
 sub mysub{
   my ($element1,$element2)=@_;
   return $element1 &#$((Some operation) $element2;
 }
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Makes for code simplicity.