A surgical system comprising: a master tool manipulator; a controller coupled to the master tool manipulator; wherein the controller is configured to: before a following mode is entered: determine an orientation misalignment, Roffset, between a first orientation of the master tool manipulator in an eye frame and an orientation of a slave instrument tip (212T, 312T) in a camera frame, cRs', and in response to a determination that the following mode is enabled and the orientation misalignment, Roffset, is less than or equal to a maximum permitted orientation error: store a transpose of the first orientation of the master tool manipulator in the eye frame mRe', store the orientation of the slave instrument tip in the camera frame, cRs', and enter the following mode; and wherein the controller is further configured to: after the following mode is entered: receive a command from the master tool manipulator to move the slave instrument tip (212T, 312T), the command indicating a second orientation of the master tool manipulator in the eye frame, eRm, generate a new slave orientation, cRs des, based on the second orientation of the master tool manipulator in the eye frame, eRm, the stored transpose of the first orientation of the master tool manipulator in the eye frame, mRe', and the stored orientation of the slave instrument tip in the camera frame, cRs', and command the system to orient the slave instrument tip (212T, 312T) based on the new slave orientation, cRs_des, wherein the desired orientation of the surgical instrument in the camera frame is defined as: cRs_des = cRs' * mRe' * eRm. a master tool manipulator; a controller coupled to the master tool manipulator; wherein the controller is configured to: before a following mode is entered: determine an orientation misalignment, Roffset, between a first orientation of the master tool manipulator in an eye frame and an orientation of a slave instrument tip (212T, 312T) in a camera frame, cRs', and in response to a determination that the following mode is enabled and the orientation misalignment, Roffset, is less than or equal to a maximum permitted orientation error: store a transpose of the first orientation of the master tool manipulator in the eye frame mRe', store the orientation of the slave instrument tip in the camera frame, cRs', and enter the following mode; and determine an orientation misalignment, Roffset, between a first orientation of the master tool manipulator in an eye frame and an orientation of a slave instrument tip (212T, 312T) in a camera frame, cRs', and in response to a determination that the following mode is enabled and the orientation misalignment, Roffset, is less than or equal to a maximum permitted orientation error: store a transpose of the first orientation of the master tool manipulator in the eye frame mRe', store the orientation of the slave instrument tip in the camera frame, cRs', and enter the following mode; and store a transpose of the first orientation of the master tool manipulator in the eye frame mRe', store the orientation of the slave instrument tip in the camera frame, cRs', and enter the following mode; and wherein the controller is further configured to: after the following mode is entered: receive a command from the master tool manipulator to move the slave instrument tip (212T, 312T), the command indicating a second orientation of the master tool manipulator in the eye frame, eRm, generate a new slave orientation, cRs des, based on the second orientation of the master tool manipulator in the eye frame, eRm, the stored transpose of the first orientation of the master tool manipulator in the eye frame, mRe', and the stored orientation of the slave instrument tip in the camera frame, cRs', and command the system to orient the slave instrument tip (212T, 312T) based on the new slave orientation, cRs_des, wherein the desired orientation of the surgical instrument in the camera frame is defined as: cRs_des = cRs' * mRe' * eRm. receive a command from the master tool manipulator to move the slave instrument tip (212T, 312T), the command indicating a second orientation of the master tool manipulator in the eye frame, eRm, generate a new slave orientation, cRs des, based on the second orientation of the master tool manipulator in the eye frame, eRm, the stored transpose of the first orientation of the master tool manipulator in the eye frame, mRe', and the stored orientation of the slave instrument tip in the camera frame, cRs', and command the system to orient the slave instrument tip (212T, 312T) based on the new slave orientation, cRs_des, wherein the desired orientation of the surgical instrument in the camera frame is defined as: cRs_des = cRs' * mRe' * eRm.