Systems and methods for reassigning control by a master controller between a plurality of teleoperational instruments is provided herein. An exemplary method includes detecting activation of an instrument reassignment input, computing proxy positions of at least a first instrument and a second instrument of the plurality of teleoperational instruments, and computing a proxy position of the master controller. The exemplary method may also include receiving input from the master controller associating the proxy position of the master controller with the proxy position of the second medical instrument and assigning control of the second instrument to the master controller based on the association between the proxy position of the master controller with the proxy position of the second instrument.
