A method for automatically creating a customized motion controller based on user input specifying desired characteristics of the motion controller. The method may compile the program into executable code and download the executable code to a target platform, thus enabling the target platform to function as the specified customized motion controller. User input may specify characteristics of the motion controller system such as: the target platform; the configuration of motors, sensors and I/O devices to be used; the supervisory control functions to be implemented; and the target language for the motion control program.