Techniques are provided for tomographic imaging with sub-beam resolution and spectral enhancement. A system implementing the techniques according to an embodiment includes a target structure comprising one or more selected materials nanopatterned on a first surface of the target structure in a selected arrangement. The system also includes a primary particle beam source to provide a particle beam incident on an area of the first surface of the target structure, the area encompassing one or more of the nanopatterned materials, such that the materials generate characteristic X-rays in response to the primary beam. The system further includes a spectral energy detector (SED) to perform individual photon counting and spectral analysis of the characteristic X-rays and estimate attenuation properties of the imaged sample. The sample is positioned both adjacent to a second surface of the target structure, opposite the first surface, and between the target structure and the SED.