Are you familiar with making mods in Minecraft? Which language do you use? It looks like serious mods are written in Java and that there are toy versions of minecraft implemented in Python which are easy to program with. There's even a Mathematica 9 implementation:
What I would do is take a simple example in one of those languages and translate it to Mathematica. A simple example in Java for the original minecraft will likely just be using Mathematica's JLink to work with Java.