A system includes first and second manipulating means, and a means for detecting mounting of an imaging means to the first manipulating means, a means for determining a first reference frame for the imaging means while the imaging means is mounted to the first manipulating means, a means for controlling a tool means relative to the first reference frame by maintaining a position and orientation of a distal portion of the tool means relative to the imaging means in the first reference frame based on a position and orientation of an input means relative to a display means, a means for detecting mounting of the imaging means to the second manipulating means, a means for determining a second reference frame for the imaging means while the imaging means is mounted to the second manipulating means, and a means for controlling the tool means relative to the second reference frame.