Thanks for the explanation and suggestions. As it turns out the root of my confusion lay in accessing the resulting array. Just for completeness sake: I needed to check the existence of a reference using defined before printing.

for my $tree (0..17) {
                for my $stem(0..10) {
                        for my $height (0..2) {
                                my $line=$mdarray[$tree][$stem][$heigh
+t];
                                if (defined @$line) {print "$tree,$ste
+m,$height : @$line \n"    }
                        }       
                }
        }
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