Once you've made a model in Rhino, you can export it into your CAM program in one of various formats; STL is the most universal. In this case your CAM program is MasterCAM, which is powerful but rather opaque for a beginner. You will tell it what controller you've got, what tool you plan to use, how fast you want to cut, etc. and define the area in which machining will take place. Then the CAM program will produce or "post" a toolpath program which is essentially a text file, that tells the CNC control program (the most common one used here is Mach3) how to move the machine in order to carve out your part.
Once you've got your machine up and running, if you still can't get your head around MasterCAM, try downloading DeskProto or FreeMill for a simplified experience of 3D toolpath generation.
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