A computer-assisted medical system comprising: a plurality of manipulators (102a, 102b); a user input system operable to generate signals to control the plurality of manipulators (102a, 102b), a portion of the user input system being movable relative to the plurality of manipulators (102a, 102b); and a controller configured to execute instructions to perform operations comprising: in a pairing mode, associating a first manipulator of the plurality of manipulators (102a, 102b) with the portion of the user input system based on movement of the portion of the user input system relative to the first manipulator being directed toward a first region defined by a location of the first manipulator, wherein the motion is detected by an accelerometer coupled to the portion of the user input system, and in a following mode, controlling motion of the first manipulator in accordance with an indication generated by the user input system in response to operation of the portion of the user input system by a user, wherein the system further comprises a sensor system configured to indicate, to the controller, a relative movement between the portion of the user input system and the first manipulator, wherein associating the first manipulator of the plurality of manipulators (102a, 102b) with the portion of the user input system comprises: associating the first manipulator with the portion of the user input system in response to the relative movement between the portion of the user input system and the first manipulator satisfying an association condition, and wherein the association condition further comprises movement of the portion of the user input system to a region within a predefined distance from the first manipulator. a plurality of manipulators (102a, 102b); a user input system operable to generate signals to control the plurality of manipulators (102a, 102b), a portion of the user input system being movable relative to the plurality of manipulators (102a, 102b); and a controller configured to execute instructions to perform operations comprising: in a pairing mode, associating a first manipulator of the plurality of manipulators (102a, 102b) with the portion of the user input system based on movement of the portion of the user input system relative to the first manipulator being directed toward a first region defined by a location of the first manipulator, wherein the motion is detected by an accelerometer coupled to the portion of the user input system, and in a following mode, controlling motion of the first manipulator in accordance with an indication generated by the user input system in response to operation of the portion of the user input system by a user, in a pairing mode, associating a first manipulator of the plurality of manipulators (102a, 102b) with the portion of the user input system based on movement of the portion of the user input system relative to the first manipulator being directed toward a first region defined by a location of the first manipulator, wherein the motion is detected by an accelerometer coupled to the portion of the user input system, and in a following mode, controlling motion of the first manipulator in accordance with an indication generated by the user input system in response to operation of the portion of the user input system by a user, wherein the system further comprises a sensor system configured to indicate, to the controller, a relative movement between the portion of the user input system and the first manipulator, wherein associating the first manipulator of the plurality of manipulators (102a, 102b) with the portion of the user input system comprises: associating the first manipulator with the portion of the user input system in response to the relative movement between the portion of the user input system and the first manipulator satisfying an association condition, and wherein the association condition further comprises movement of the portion of the user input system to a region within a predefined distance from the first manipulator. associating the first manipulator with the portion of the user input system in response to the relative movement between the portion of the user input system and the first manipulator satisfying an association condition, and wherein the association condition further comprises movement of the portion of the user input system to a region within a predefined distance from the first manipulator.