Method of determining an overlay error between device layers of a multilayer semiconductor device using an atomic force microscopy system, wherein the semiconductor device comprises a stack of device layers comprising a first patterned layer and a second patterned layer, and wherein the atomic force microscopy system comprises a probe tip, wherein the method comprises: moving the probe tip and the semiconductor device relative to each other for scanning of the surface; and monitoring motion of the probe tip with tip position detector during said scanning for obtaining an output signal; during said scanning, applying a first acoustic input signal to at least one of the probe or the semiconductor device; analyzing the output signal for mapping at least subsurface nanostructures below the surface of the semiconductor device; and determining the overlay error between the first patterned layer and the second patterned layer based on the analysis.