Minecraft

I am looking to learn Java, and the best way I learn is through practical situations. I have decided to make a game extremely similar to "Minecraft". If you do not know what this is then please google it. I was wondering if anyone could tell me where I should start and if they could point me in the right direction. I want to create it from scratch without copying any of the Minecraft original code, I don't mind if it ends up the same I just want to find my way there rather than doing a copy and paste job.

I'm sorry, but unless you've got experience in mastering programming languages, I highly doubt you will be writing anything which resembles mine-craft for a very long time.
You're going to need to start from the beginning, which would be Sun/Oracle's tutorials (found here) - and unless you jump right in at the deep end, which I highly recommend you don't, you're going to be writing a lot of console based programs to help you learn - and not interactive GUI's.

Good luck with making a game which has supplied Notch with his millions ;)

I do believe that Notch used lwjgl game framework, which in turn uses a 1:1 (almost) implementation of c interface to opengl.

So this is how your learning path would probably look like.
- Java intermediate / advanced level
- Linear Algebra to a pretty decent level - college class atleast
- Opengl theory (atleast the basic understanding of the pipeline abstraction).
- Shader technology incl. a shader language glsl.

Thats really a lot, but then again, Notch is now a very very rich man