Atomic force microscopy device (110a,...,110n), the device comprising a scan head, the scan head including a probe, the probe comprising a flexible carrier and a probe tip arranged on the flexible carrier, wherein the atomic force microscopy device is arranged for determining sub-surface structures in a sample, wherein the atomic force microscopy device further comprises: an actuator cooperating with at least one of the scan head or a substrate holder for moving the probe tip and the sample relative to each other in one or more directions parallel to a surface of the sample for scanning of the surface with the probe tip; a tip position detector for measuring motion of the probe tip relative to the scan head during said scanning, the detector being arranged for providing an output signal indicative of said motion; and a controller for receiving and analyzing the output signal from the tip position detector; wherein the atomic force microscopy device further comprises: a first actuator for applying a first acoustic input signal comprising a signal component at a first frequency to at least one of the probe or the sample; wherein the controller is arranged for analyzing the output signal for mapping at least subsurface nanostructures below the surface of the sample, wherein the probe tip has an end portion with an end facing away from said flexible carrier, wherein said end portion has a largest cross-section with a cross-sectional area Acx, a square root of which is at least 100 nm and wherein a distance Dend between said end and said largest cross-section is at most two times the value of said square root, characterized in that said controller comprises a first processing module for reconstructing a feature signal (Sdm) from said output signal (Sscan), wherein said feature signal (Sdm) is a demodulated signal (Sdm), a second processing module for low-pass filtering said feature signal and for providing a low-pass filtered signal (S LP) and according to a first option further comprising a centroid identification module detecting a centroid position (Scentr) in said low-pass filtered signal S LP and rendering an output signal (Scentr) indicating the centroid position as a position of a detected sub-surface feature or according to a second option further comprising a curve fitting module to perform curve fitting on the demodulated signal (Sdm) based on an input signal (Ser) specifying an expected response curve for a marker present as a sub-surface structure in the sample, and to provide an output signal (Smp) indicative for a position of the marker estimated therewith. an actuator cooperating with at least one of the scan head or a substrate holder for moving the probe tip and the sample relative to each other in one or more directions parallel to a surface of the sample for scanning of the surface with the probe tip; a tip position detector for measuring motion of the probe tip relative to the scan head during said scanning, the detector being arranged for providing an output signal indicative of said motion; and a controller for receiving and analyzing the output signal from the tip position detector; a first actuator for applying a first acoustic input signal comprising a signal component at a first frequency to at least one of the probe or the sample; wherein the controller is arranged for analyzing the output signal for mapping at least subsurface nanostructures below the surface of the sample, wherein the probe tip has an end portion with an end facing away from said flexible carrier, wherein said end portion has a largest cross-section with a cross-sectional area Acx, a square root of which is at least 100 nm and wherein a distance Dend between said end and said largest cross-section is at most two times the value of said square root, characterized in that said controller comprises a first processing module for reconstructing a feature signal (Sdm) from said output signal (Sscan), wherein said feature signal (Sdm) is a demodulated signal (Sdm), a second processing module for low-pass filtering said feature signal and for providing a low-pass filtered signal (S LP) and according to a first option further comprising a centroid identification module detecting a centroid position (Scentr) in said low-pass filtered signal S LP and rendering an output signal (Scentr) indicating the centroid position as a position of a detected sub-surface feature or according to a second option further comprising a curve fitting module to perform curve fitting on the demodulated signal (Sdm) based on an input signal (Ser) specifying an expected response curve for a marker present as a sub-surface structure in the sample, and to provide an output signal (Smp) indicative for a position of the marker estimated therewith.