Biodynamic feedthrough in a master control system can be mitigated. An accelerometer is used to measure the acceleration of an environment. In one embodiment, mitigation damping forces can then be determined based on the velocity of an effector of a haptic manipulator and the measured accelerations. The haptic manipulator applies the mitigation damping forces as force feedback. In another embodiment, biodynamic feedthrough can be filtered from the input signal. Parameters for a model can be accessed based on the position of the effector, and the model can be used to predict biodynamic feedthrough from the measured accelerations.