A method, a non-transitory computer readable medium, and an apparatus for operating the robotic control system comprising a master apparatus (64) in communication with an input device (58, 60) having a handle (102) and a slave system (54, 74) having a tool (66, 67) having an end effector (73) whose position and orientation is determined in response to a current position and current orientation of the handle. The method involves producing a desired end effector position and orientation in response to a current position and orientation of the handle. The method involves causing the input device to provide haptic feedback that impedes translational movement of the handle, while permitting rotational movement of the handle and preventing movement of the end effector, when a rotational alignment difference between the handle and the end effector meets a disablement criterion. The method further involves re-enabling translational movement of the handle when the rotational alignment difference meets an enablement criterion.
