Techniques for retracting an instrument into an entry guide include receiving a retraction command for the instrument, the retraction command commanding movement of the instrument into the entry guide; causing, in response to the retraction command and using an instrument manipulator, movement of a rotational joint of the instrument that is external to the entry guide toward a distal end of the entry guide; actuating, after the rotational joint reaches a minimum distance from the distal end of the entry guide, the rotational joint to orient a link of the instrument so that the link can be retracted into the entry guide, the link being adjacent to and distal to the rotational joint; and causing, after the link is oriented so that the link can be retracted into the entry guide and using the instrument manipulator, further movement of the rotational joint toward the distal end of the entry guide.