This document relates to a method of performing surface measurements on a surface of a sample using a scanning probe microscopy system. The system comprises a sample support structure for supporting a sample, a sensor head including a probe comprising a cantilever and a probe tip arranged on the cantilever, and an actuator for scanning the probe tip relative to the substrate surface for mapping of the nanostructures. The method comprising the steps of: vibrating the cantilever using an actuator and moving the probe relative to the substrate surface for performing said scanning. The probe is held at a distance to the substrate surface such as to allow contact at a plurality of intermittent contact moments between the probe tip and the surface during said vibrating of the cantilever. The steps of vibrating of the cantilever and moving of the probe are performed concurrently. For performing the surface measurements, the method comprises obtaining a sensor signal indicative of a position of the probe tip during said scanning, and analyzing this signal by quantifying two or more frequency components in a Fourier transform for determining an estimate of a force value of a force between said substrate surface and said probe tip during said contact moments.