A system for communicating with a motion controller, comprising a set of primitive motion commands and non-primitive motion commands, a set of motion operations, a reprogrammable motion controller capable of executing at least one motion command, a set of selectable software modules, and a software system. Functionality of the non-primitive motion commands can be emulated by a combination of primitive motion commands. Functionality of the primitive motion commands cannot be emulated by a combination of primitive motion commands. At least one motion operation is associated with at least one motion command. At least one software module is associated with at least one motion controller, and at least two selectable software modules expose a common software interface. The software system is capable of commanding at least one motion controller to perform at least one motion operation using the common software interface exposed by at least one selected software module associated with at least one motion controller.