Most CNC machines will accept commands written by third-party software. The way it typically works is that a model is created in a CAD program which is fed to a CAM program, which produces a G-code program which is essentially a text file. This is loaded into the program ( EMC, Mach3, or another proprietary control program) that actually runs the machine. If Matlab is producing directional commands, you can translate them into G-code pretty easily, and load them into the program controlling the CNC machine.
I don't think you can get your software package to directly control the CNC; that would require a lot of sophisticated coding, especially on a Windows platform. But if all you need is for the machine to execute some directional commands, that shouldn't be a problem using one of the CNC control programs already written and functional.
Or am I missing something?
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