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Fabrication of semiconductor heterostructures is now so precise that metrology has become a key challenge for progress in science and applications. It is now relatively straightforward to characterize classic III-V and group IV heterostructures consisting of slabs of different semiconductor alloys with thicknesses of 5 nm and greater using sophisticated tools such as X-ray diffraction, high energy X-ray photoemission spectroscopy, and secondary ion mass spectrometry. However, profiling thin layers with nm or sub-nm thickness, e.g. atomically thin dopant layers (-layers), of impurities required for modulation doping and spin-based quantum and classical information technologies is more challenging. Here, we present theory and experiment showing how resonant-contrast X-ray reflectometry meets this challenge. The technique takes advantage of the change in the scattering factor of atoms as their core level resonances are scanned by varying the X-ray energy. We demonstrate the capability of the resulting element-selective, non-destructive profilometry for single arsenic -layers within silicon, and show that the sub-nm electronic thickness of the -layers corresponds to sub-nm chemical thickness. In combination with X-ray fluorescence imaging, this enables non-destructive three-dimensional characterization of nano-structured quantum devices. Due to the strong resonances at soft X-ray wavelengths, the technique is also ideally suited to characterize layered quantum materials, such as cuprates or the topical infinite-layer nickelates.