The invention is directed at a method of performing scanning probe microscopy on a substrate surface using a scanning probe microscopy system, the system including at least one probe head, the probe head comprising a probe tip arranged on a cantilever and a tip position detector for determining a position of the probe tip along a z-direction transverse to an image plane, the method comprising: positioning the at least one probe head relative to the substrate surface; moving the probe tip and the substrate surface relative to each other in one or more directions parallel to the image plane for scanning of the substrate surface with the probe tip; and determining the position of the probe tip with the tip position detector during said scanning for mapping nanostructures on the substrate surface; wherein said step of positioning is performed by placing the at least one probe head on a static carrier surface.