The properties of atomically thin materials essentially depend on their structures, including impurities, defects and interfaces with underlying substrates. Thus, the detailed structural information is relevant for creation of 2D materials with desired properties. Here, we explore the capabilities of photoelectron diffraction and holography for structural analysis of atomically thin layers using as examples such systems as h-BN, graphene, and modified graphene with boron impurities. We show that for planar 2D crystals with commensurate interface to the substrate, it is possible to visualize the interface and impurities with high spatial resolution, and to distinguish possible non-equivalent structural units. Our approach applied to B-doped graphene on Ni(1 1 1) and Co(0 0 0 1) surfaces has allowed to reveal asymmetry of boron concentrations in the two carbon sublattices and established its dependence on the applied synthesis procedure and chosen substrate. The obtained results suggest that such approach can be widely applied for studies of various 2D systems, where the structures of interfaces and defects are of remarkable importance.