The error message means that you are trying to dereference a scalar as that does not contain a reference.

You are attempting to deref two arrays, $MyArrayOfArrays, and $MyArrayOfArrays[$i]. One of them doesn't have the value you expect it to have. Look at the last place you assigned to these variables. You may also want to try using Data::Dumper to inspect the structure.

I highly recommend reading and rereading perldsc and perlreftut.

Update: Since I was so terribly slow posting my advice, I thought I'd add an additional comment in an attempt to make this node useful.

You got this error because you are using strict. If you weren't using strict, the error message would disappear and your script would run just fine. Except that it wouldn't work. You'd be working with arrays named @1 or @3 or whatever. If you're lucky, you'd wind up with weirdly mangled output and have one hell of a time figuring out what the problem was. Even worse, everything might seem to work just fine...

I congratulate you on choosing to use strict, and sticking with it, despite getting these error messages. Keep up the good work.