A controller operates in different operating modes to control movement of a distal tip of a medical instrument when inserting and retracting the medical instrument through linked body passages. When inserting the medical instrument, the controller normally operates in an automatic navigation mode unless manually overridden to operate in a manual mode. When retracting the medical instrument, the controller normally operates in a zero-force mode to allow the distal tip to freely move so that it may comply with the shape of the passages as the medical instrument is being retracted through the linked body unless manually overridden to operate in a manual mode.