A method computes reference signals for a machine with redundant positioning by first generating a reference trajectory according to an ordered list of points. Then, using a filter or by choosing the value of the reference at each sampling time, a reference trajectory for the slow subsystem is produced. Next, determine whether the reference trajectory and the slow subsystem reference trajectory violate feasibility constraints, and if true, slowing down the reference trajectory and repeating with the generation of the slow subsystem reference trajectory. The slow subsystem reference trajectory is sent, via a model predictive control block, to a slow positioning subsystem controller, and a combination of the slow subsystem reference trajectory and the reference trajectory is sent to a fast positioning subsystem controller.