A medical system comprising: a manipulator assembly (304, 504) having a plurality of links (324, 326, 330) extending between an instrument holder (320, 518) and a proximal base (302, 510), the instrument holder (320, 518) being configured to support an instrument (306, 508) having an instrument shaft extending through an access site of a patient, the manipulator assembly (304, 504) being configured for moving the instrument relative to the proximal base (302, 510) when the instrument is supported by the instrument holder (320, 518), wherein the plurality of links (324, 326, 330) are interconnected by a plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8), and wherein the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) provide sufficient degrees of freedom to allow a range of joint states for a given state of the instrument when the instrument is supported by the instrument holder (320, 518); characterized in further comprising a processor configured to: determine a first set of joint movements of the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) that maintains the instrument shaft at the access site during movement of the access site, and determine a second set of joint movements of the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) that, when combined with the first set of joint movements, maintains an orientation or a pose of at least a portion of the manipulator assembly (304, 504) during the movement of the access site. a manipulator assembly (304, 504) having a plurality of links (324, 326, 330) extending between an instrument holder (320, 518) and a proximal base (302, 510), the instrument holder (320, 518) being configured to support an instrument (306, 508) having an instrument shaft extending through an access site of a patient, the manipulator assembly (304, 504) being configured for moving the instrument relative to the proximal base (302, 510) when the instrument is supported by the instrument holder (320, 518), wherein the plurality of links (324, 326, 330) are interconnected by a plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8), and wherein the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) provide sufficient degrees of freedom to allow a range of joint states for a given state of the instrument when the instrument is supported by the instrument holder (320, 518); characterized in further comprising a processor configured to: determine a first set of joint movements of the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) that maintains the instrument shaft at the access site during movement of the access site, and determine a second set of joint movements of the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) that, when combined with the first set of joint movements, maintains an orientation or a pose of at least a portion of the manipulator assembly (304, 504) during the movement of the access site. determine a first set of joint movements of the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) that maintains the instrument shaft at the access site during movement of the access site, and determine a second set of joint movements of the plurality of joints (J1, J2, J3, J4, J5, J6, J7, J8) that, when combined with the first set of joint movements, maintains an orientation or a pose of at least a portion of the manipulator assembly (304, 504) during the movement of the access site.