A system and method for shaping the trajectory of a motion command to reduce the effects of a load on performance of a motor dynamically modifies the motion profile in real time to limit the reference signals in the motion profile to feasible commands. A load observer determines an estimated disturbance acceleration. The estimated disturbance acceleration includes the dynamics of the controlled load and is used to modify a maximum and a minimum limit for the acceleration reference. The acceleration limits are, in turn, used to determine velocity limits. The motion profile and modified acceleration and velocity limits are provided to a state filter which determines a new motion profile for use by the motor drive to control operation of a motor and to control the load connected to the motor.