Method of controlling frequency modulated-atomic force microscope

A method is provided for controlling an FM-AFM including a cantilever having a resonant frequency and an excitation system configured to oscillate the cantilever in response to a drive signal. The method includes determining latency of the excitation system; receiving a deflection signal indicating a deflection of a cantilever tip; mixing the deflection signal with a first sine signal output by a PLL indicating a frequency shift of a frequency response of the cantilever; measuring the frequency shift in response to the drive signal; determining spurious phase of the cantilever based on the determined latency, the resonant frequency of the cantilever, and the measured frequency shift; providing a second sine signal having a phase that is advanced by the determined spurious phase to preemptively compensate for subsequent spurious phase of the cantilever; and driving the excitation system using the second sine signal with an adjusted amplitude as the drive signal.