You probably want to examine perlreftut, but here are some thoughts. I'm not sure just how familiar you are with Perl, so you might want to check perldata just to see the datatypes (specifically, hashes and arrays). You may want to read those before proceeding with this post

That being said, you could represent this many ways.

1. A 3D array, as you say, which would actually be an array of array references of array references. A possibility, but probably unnecessary, as your indices would be x,y,beans - and that would probably waste space (i.e. sparse)
2. An array of hashrefs - this could contain something like an object. Each hashref could have the keys "x", "y" and "beans" and those values individually.
3. Some combination of the two, e.g. an array of hasherefs of arrayrefs . Keys being "coordinates" (value of arrayref) and "beans" ( value being scalar)

I'm sure there are many more ways to represent this, but just don't want you to get "stuck" into thinking of just arrays. Perl is much more fun than that :)