This document relates to a method of tuning a scanning probe microscopy system and system therefore. The system comprising a sample carrier and a probe with a probe tip, and is configured for positioning the probe tip relative to a sample. The system further includes a transducer, a sensor for sensing probe tip vibrations, and a controller. The method comprises: a) applying an acoustic vibration signal comprising a first frequency and a second frequency to the sample; b) at a first position of the probe tip, controlling the transducer to sweep the first frequency across a first frequency range, and obtaining a first probe tip sensor signal; c) at a second position of the probe tip, controlling the transducer to sweep the first frequency across at least said first frequency range, and obtaining a second probe tip sensor signal; d) analyzing the first and second sensor signal to obtain a difference characteristic dependent on the first frequency, and selecting a first frequency value for which the difference characteristic exceeds a threshold for tuning the first frequency. The first and second position are selected such that a subsurface structure of the sample at the first and second position is different.