Umm, well, there really is no right way. But there really isn't a wrong way either... Use your imagination! Get like three old Parallel(interfaced) printers, as i am sure you can get them almost for free. Then, get a dremel tool(not sure how spendy they are. i don't own one, yet), and make an X,Y,Z axis. Pretty simple if you ask me.
Make a circuit to control the stepper motors, and then write software. Heck, you could go RS232, or SPP(standard parallel port), or EPP, or ECP.
Let your mind run free! If you don't get a good mark(grade) on it, you will still have an awesome machine to make custom parts from, and you would have learned a hell of a lot of info. That is really the only reason for the final year projects, isn't it? To see what you are capable of? Yeah...