A method of operating a metrology instrument includes generating relative motion between a probe and a sample at a scan frequency using an actuator. The method also includes detecting motion of the actuator using a position sensor that exhibits noise in the detected motion, and controlling the position of the actuator using a feedback loop and a feed forward algorithm. In this embodiment, the controlling step attenuates noise in the actuator position compared to noise exhibited by the position sensor over the scan bandwidth. Scan frequencies up to a third of the first scanner resonance frequency or greater than 300 Hz are possible.