A system and method of maintaining a tool pose for a computer-assisted medical device with an articulated arm including one or more first joints and one or more second joints, a tool distal to the first joints and the second joints, and a control unit coupled to the first joints and the second joints. The control unit maintains a pose of the tool during movement of the first joints using the second joints by determining a reference coordinate frame for the tool, determining a reference transform of the tool in the reference coordinate frame prior to the movement of the first joints, determining an actual transform of the tool in the reference coordinate frame while the first joints are being moved, determining differences between the reference transform and the actual transform, and maintaining the pose of the tool by driving the second joints based on the differences.