A medical robotic system includes an entry guide with articulatable instruments extending out of its distal end, an entry guide manipulator providing controllable four degrees-of-freedom movement of the entry guide relative to a remote center, and a controller configured to manage operation of the entry guide manipulator in response to operator manipulation of one or more input devices. As the entry guide manipulator approaches a yaw/roll singularity, the controller modifies its operation to allow continued movement of the entry guide manipulator without commanding excessive joint velocities while maintaining proper orientation of the entry guide.
