Method of performing subsurface imaging of one or more embedded structures in a substrate underneath a substrate surface, the method being performed using an atomic force microscopy system, wherein the atomic force microscopy system comprises a probe with at least one probe tip, and a sensor for sensing a position of the probe tip for detecting probe tip motion, the method comprising the steps of: positioning the probe tip relative to the substrate for establishing contact between the probe tip and the substrate surface; applying, using at least one first signal application actuator (70, 27), a first acoustic input signal to the substrate; applying, using at least one second signal application actuator, a second acoustic input signal to the substrate; detecting, using the sensor, an output signal from the substrate in response to the first and second acoustic input signal; and analyzing the output signal for obtaining information on the embedded structures, for enabling imaging thereof; wherein the at least one probe comprises a plurality of probe tips forming a probe tip array, wherein during the step of positioning the probe is positioned such as to establish contact between the substrate surface and each of the probe tips; wherein 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 as to provide, in the output signal, one of: a return signal including a scattered fraction of the second acoustic input signal scattered from the embedded structures; or a transmitted second acoustic input signal whose wave-front is distorted due to scattering from the embedded structures. positioning the probe tip relative to the substrate for establishing contact between the probe tip and the substrate surface; applying, using at least one first signal application actuator (70, 27), a first acoustic input signal to the substrate; applying, using at least one second signal application actuator, a second acoustic input signal to the substrate; detecting, using the sensor, an output signal from the substrate in response to the first and second acoustic input signal; and analyzing the output signal for obtaining information on the embedded structures, for enabling imaging thereof; wherein the at least one probe comprises a plurality of probe tips forming a probe tip array, wherein during the step of positioning the probe is positioned such as to establish contact between the substrate surface and each of the probe tips; wherein 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 as to provide, in the output signal, one of: a return signal including a scattered fraction of the second acoustic input signal scattered from the embedded structures; or a transmitted second acoustic input signal whose wave-front is distorted due to scattering from the embedded structures. a return signal including a scattered fraction of the second acoustic input signal scattered from the embedded structures; or a transmitted second acoustic input signal whose wave-front is distorted due to scattering from the embedded structures.