The document relates to a method of performing subsurface imaging of embedded structures underneath a substrate surface, using an atomic force microscopy system. The system comprises a probe with a probe tip, and a sensor for sensing a position of the probe tip. The method comprises the steps of: positioning the probe tip relative to the substrate: applying a first acoustic input signal to the substrate; applying a second acoustic input signal to the substrate; detecting an output signal from the substrate in response to the first and second acoustic input signal; and analyzing the output signal. The first acoustic input signal comprises a first signal component and a second signal component, the first signal component comprising a frequency below 250 megahertz and the second signal component either including a frequency below 2.5 megahertz or a frequency such as to provide a difference frequency of at most 2.5 megahertz with the first signal component, such as to enable analysis of an induced stress field in the substrate; and wherein the second acoustic input signal comprises a third signal component having a frequency above 1 gigahertz, such that the return signal includes a scattered fraction of the second acoustic input signal scattered from the embedded structures. This enables to perform imaging a various depths in one pass, across a large range of depths.