A method of operating a robotic control system comprising a master apparatus in communication with an input device having a handle and a slave system having a tool having an end effector whose position and orientation is determined in response to a position and orientation of the handle. The method involves producing a desired end effector position and a desired end effector orientation of the end effector, in response to a current position and a current orientation of the handle. The method further 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 first criterion. The method further involves re-enabling translational movement of the handle when the rotational alignment difference meets a second criterion.