Methods and systems for subsurface imaging of nanostructures buried inside a plate shaped substrate are provided. An ultrasonic generator at a side face of the substrate is used to couple ultrasound waves (W) into an interior of the substrate. The interior has or forms a waveguide for propagating the ultrasound waves (W) in a direction (X) along a length of the substrate transverse to the side face. The nanostructures are imaged using an AFM tip to measure an effect (E) at the top surface caused by direct or indirect interaction of the ultrasound waves (W) with the buried nanostructures.