A minimally invasive surgical system configured to teleoperate a slave surgical instrument, the minimally invasive surgical system comprising: a master grip; and a control system configured to be coupled to the master grip and to the slave surgical instrument, and configured to control movement of the slave surgical instrument in dependence upon movements of the master grip; wherein the control system is configured to reduce an alignment error between the master grip and the slave surgical instrument using an iterative process including: i) determining a new alignment error between a new orientation of the master grip and a current orientation of the slave surgical instrument, ii) updating a stored current alignment error with the new alignment error in response to determining that the new alignment error is less than the stored current alignment error, iii) generating a new slave orientation based on the new orientation of the master grip and the stored current alignment error, iv) determining a commanded angular velocity for the slave surgical instrument from a sensed angular velocity of the master grip; v) introducing a control system error between the orientation of the master grip and the orientation of the slave surgical instrument by adjusting the commanded angular velocity of the slave surgical instrument to penalize the commanded angular velocity of the slave surgical instrument based on the current alignment error, and vi) generating a command for commanding movement of the slave surgical instrument, the command including the new slave orientation and the penalized commanded angular velocity, wherein penalizing the commanded angular velocity uses an angular velocity scale factor which decreases with an increase of a magnitude of the current alignment error. a master grip; and a control system configured to be coupled to the master grip and to the slave surgical instrument, and configured to control movement of the slave surgical instrument in dependence upon movements of the master grip; wherein the control system is configured to reduce an alignment error between the master grip and the slave surgical instrument using an iterative process including: i) determining a new alignment error between a new orientation of the master grip and a current orientation of the slave surgical instrument, ii) updating a stored current alignment error with the new alignment error in response to determining that the new alignment error is less than the stored current alignment error, iii) generating a new slave orientation based on the new orientation of the master grip and the stored current alignment error, iv) determining a commanded angular velocity for the slave surgical instrument from a sensed angular velocity of the master grip; v) introducing a control system error between the orientation of the master grip and the orientation of the slave surgical instrument by adjusting the commanded angular velocity of the slave surgical instrument to penalize the commanded angular velocity of the slave surgical instrument based on the current alignment error, and vi) generating a command for commanding movement of the slave surgical instrument, the command including the new slave orientation and the penalized commanded angular velocity, i) determining a new alignment error between a new orientation of the master grip and a current orientation of the slave surgical instrument, ii) updating a stored current alignment error with the new alignment error in response to determining that the new alignment error is less than the stored current alignment error, iii) generating a new slave orientation based on the new orientation of the master grip and the stored current alignment error, iv) determining a commanded angular velocity for the slave surgical instrument from a sensed angular velocity of the master grip; v) introducing a control system error between the orientation of the master grip and the orientation of the slave surgical instrument by adjusting the commanded angular velocity of the slave surgical instrument to penalize the commanded angular velocity of the slave surgical instrument based on the current alignment error, and vi) generating a command for commanding movement of the slave surgical instrument, the command including the new slave orientation and the penalized commanded angular velocity, wherein penalizing the commanded angular velocity uses an angular velocity scale factor which decreases with an increase of a magnitude of the current alignment error.