A method of operating a robotic control system comprising a master apparatus in communication with a plurality of input devices having respective handles capable of translational and rotational movement and a slave system having a tool positioning device corresponding to each respective handle and holding a respective tool having an end effector whose position and orientation is determined in response to a position and orientation of a corresponding handle. The method involves producing desired new end effector positions and orientations of respective end effectors in response to current positions and current orientations of corresponding handles. using the desired new end effector positions and orientations to determine distances from each point of a first plurality of points along a first tool positioning device to each point of a plurality of points along at least one other tool positioning device, and determining and notifying that any of the distances meets a proximity criterion.
