The invention is directed at a method of performing scanning probe microscopy on a substrate surface using a scanning probe microscopy system. A probe tip and substrate surface are moved relative to each other in one or more directions parallel to the scanning plane to position the probe tip to a scanning position on the substrate surface with the probe tip; a displacement is measured by an encoder of said probe tip in said one or more directions; and a fiducial pattern is provided fixed relative to the substrate surface, said fiducial pattern having a scannable structure that is scannable by said probe tip and said structure forming a grid of fiducial marks in said one or more dimensions; said grid dimensioned to allow for measuring placement deviations of the probe tip relative to the probe head by identifying one or more fiducial marks in the fiducial pattern.