A computer-assisted system includes a manipulator assembly configured to couple to a cannula at a distal portion of the manipulator assembly. The cannula has a lumen configured to receive a shaft of an instrument. A cannula axis is aligned with the cannula when the cannula is coupled to the manipulator assembly. An instrument axis is aligned with the instrument when the instrument is coupled to the manipulator assembly. A controller coupled to the manipulator assembly is configured to receive an indication to reposition a remote center of motion (RCM) for the manipulator assembly while the RCM is positioned at a first location relative to the distal portion along an axis, wherein the axis is aligned with the cannula axis or the instrument axis; and in response to receiving the indication, cause the RCM to be positioned at a second location relative to the distal portion along the axis.