Scanning probe microscopy (SPM) represents a powerful tool that, in the past 30 years, has allowed for the investigation of material surfaces in unprecedented ways at the nanoscale level. However, SPM has shown very little capability for depth penetration, which several nanotechnology applications require. Subsurface imaging has been achieved only in a few cases, when subsurface features influence the physical properties of the surface, such as the electronic states or the heat transfer. Ultrasonic force microscopy (UFM), an adaption of the contact mode atomic force microscopy, can dynamically measure the stiffness of the elastic contact between the probing tip and the sample surface. In particular, UFM has proven highly sensitive to the near-surface elastic field in non-homogeneous samples. In this paper, we present an investigation of two-dimensional (2D) materials, namely flakes of graphite and molybdenum disulphide placed on structured polymeric substrates. We show that UFM can non-destructively distinguish suspended and supported areas and localise defects, such as buckling or delamination of adjacent monolayers, generated by residual stress. Specifically, UFM can probe small variations in the local indentation induced by the mechanical interaction between the tip and the sample. Therefore, any change in the elastic modulus within the volume perturbed by the applied load or the flexural bending of the suspended areas can be detected and imaged. These investigation capabilities are very promising in order to study the buried interfaces of nanostructured 2D materials such as in graphene-based devices.