A system includes a master manipulator and a controller. The controller determines, before the system enters a following mode, a relative orientation between an orientations of an axis of the master manipulator in an eye frame and a corresponding axis of a slave instrument tip in a camera frame. After the system enters the following mode, the controller determines whether an orientation misalignment between the orientations of the axis of the master manipulator and the corresponding axis of the slave instrument tip is less than or equal to a maximum permitted orientation error. When the orientation misalignment is less than or equal to the maximum permitted orientation error, the controller receives a command indicating a desired orientation of the slave instrument tip from the master manipulator and commands the system to orient the slave instrument tip based on the desired orientation of the slave instrument tip and the relative orientation.
