This document is directed at a method of manufacturing a semiconductor element, the method comprising manipulating a surface of a substrate using an atomic force microscope, the atomic force microscope including a probe, the probe including a cantilever and a probe tip, the substrate including at least one or more device features embedded underneath the surface. The method comprises: imaging the embedded device features, and identifying that a position of the probe tip of the atomic force microscope is aligned with the feature; and displacing the probe tip transverse to the surface for exerting a stress for performing the step of surface manipulation, as for example contact holes. Imaging is performed by applying and obtaining an acoustic signal to and from the substrate via the probe tip, including a first and a second signal component at different frequencies. The imaging and surface manipulation are performed using said same probe and probe tip.