This paper reports on the implementation of electron tomography in the Scanning Electron Microscope, describing its application in both physical and biological sciences. The experimental set up for tomography is described with emphasis on the scanning-transmission imaging modality, which allows one to record a series of projective images of a thin specimen. The computation of the three-dimensional arrangement of the constituents in graphene-ZnO nanorods and in collagen fibrils in dermal tissue is discussed. In addition, we show how the implementation of a compressed sensing approach can be useful to preserve nanometric resolution and overcome the limitations of the experimental strategy.