A surgical manipulator operates in a manual mode in which a user applies forces and torques to the surgical instrument to cause movement of the energy applicator. The surgical manipulator also operates in a semi-autonomous mode in which the surgical manipulator moves the energy applicator along a tool path. A controller monitors output of a force/torque sensor as the energy applicator is being moved along the tool path in the semi-autonomous mode and transitions from the semi-autonomous mode to the manual mode in response to the output exceeding a limit.