Basically I want a loop to check for each value in an array, if each scalar is greater than zero. If so, I want to do something with the corresponding value in a 2nd array.

perhaps the answer to your homework looks like:

| 
| handwaving here... starting with @ry1 and @ry2 being fully populated
+.
for($i=0;$i<=($#ry1 < $#ry2? $#ry1 : $#ry2){
    if ($ry1[$i] != 0 ) {
             $ry[$i] = <do something> # edit accordingly
    }
}
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I'm not too sure what your first paragraph is about, it confuses me.