A method of operating a medical system comprising an entry guide, an articulated instrument, a manipulator, and a processor, the articulated instrument having a plurality of links, wherein adjacent links of the plurality of links are coupled together by a rotary joint, and wherein the articulated instrument is configured to be coupled to the manipulator so that a most proximal link of the plurality of links is at least partially disposed within the entry guide and a most distal link of the plurality of links is configured to retract into, and extend out of, the entry guide, the method comprising:
- determining, using the processor, a current mode of the medical system, the current mode being one of a plurality of modes including a retraction mode;
- and
- conditioned upon the current mode being the retraction mode:
- allowing, using the processor, a part of the manipulator to be manually moved so that when the articulated instrument is coupled to the manipulator, the most proximal link moves in a direction along a longitudinal axis of the most proximal link;
- and
- causing, using the processor, at least one of the adjacent links to be rotated about the rotary joint in response to the part of the manipulator being manually moved, so that longitudinal axes of the adjacent links are substantially in line with the longitudinal axis of the most proximal link prior to the adjacent links entering the entry guide.