Multilayer structures of active semiconductor devices (1), novel memories (2) and semiconductor interconnects are becoming increasingly three-dimensional (3D) with simultaneous decrease of dimensions down to the few nanometres length scale (3). Ability to test and explore these 3D nanostructures with nanoscale resolution is vital for the optimization of their operation and improving manufacturing processes of new semiconductor devices. While electron and scanning probe microscopes (SPMs) can provide necessary lateral resolution, their ability to probe underneath the immediate surface is severely limited. Cross-sectioning of the structures via focused ion beam (FIB) to expose the subsurface areas often introduces multiple artefacts that mask the true features of the hidden structures, negating benefits of such approach. In addition, the few tens of micrometre dimension of FIB cut, make it unusable for the SPM investigation.