Conductive atomic force microscopy was used to image permalloy nanostructures embedded in Al2O3. Two layers of permalloy nanostructures embedded in Al2O3 were fabricated in a stacked manner using nanosphere lithography and electron beam evaporation. Bias dependence conduction of the bottom and top layers of the permalloy nanostructures was demonstrated. A simple phenomenological model based on thermionic emission, direct tunnelling and Fowler-Nordheim tunnelling was used to explain the experimental findings. When applied to Co-HfO2 granular films, the technique enabled 3D reconstructed images of the films to obtain grain size information in a non-destructive manner. This relatively simple and cost-effective technique has the potential to be developed to image nanostructures and devices tomographically.