As a general advice, pick variable names that clearly and specifically describe what they contain. In the long run (e.g. when you need to look at the code again in several months), that will keep things easier for you.

For a sub in which you calculate volumes and/or areas and the like, you can probably suffice with more 'generic' names such as $length, $width, $height, etc.
In your main program, you're more likely to deal with various lengths, heights, etc. For those, I would recommend naming them (for example) $box_width, $box_length, etc. if they're describing a box.

As you mentioned, little prevents you from scoping the variables and naming them similarly. Do as you prefer, of course, but from a maintainability perspective I recommend you make things stand out (i.e. use different names).