A method to perform sub-surface detection of nanostructures in a sample, uses an atomic force microscopy system that comprising a scan head having a probe with a cantilever and a probe tip arranged on the cantilever. The method comprises: moving the probe tip and the sample relative to each other in one or more directions parallel to the surface for scanning of the surface with the probe tip; and monitoring motion of the probe tip relative to the scan head with a tip position detector during said scanning for obtaining an output signal. During said scanning acoustic vibrations are induced in the probe tip by applying a least a first and a second acoustic input signal respectively comprising a first and a second signal component at mutually different frequencies above IGHz, differing by less than IGHz to the probe, and analyzing the output signal for mapping at least subsurface nanostructures below the surface of the sample.