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X-ray photoelectron diffraction is a unique tool and the only choice to probe local atomic structure of 2D materials and buried interfaces. Both graphene and topological insulators (TIs) present a fundament for future electronics and spintronics. Using photoelectron diffraction and spectroscopy we have demonstrated a selective incorporation of boron impurities into only one of the two graphene sublattices. We have shown that in the well-oriented graphene on the Co(0001) surface the carbon atoms occupy two nonequivalent positions with respect to the Co lattice, namely top and hollow sites. Boron impurities embedded into the graphene lattice preferably occupy the hollow sites due to a site-specific interaction with the Co pattern. Our theoretical calculations predict that such boron-doped graphene possesses a band gap that can be precisely controlled by the dopant concentration. B-graphene with doping asymmetry is, thus, a novel material, which is worth considering as a good candidate for electronic applications. We characterized the atomically precise interface between Fe,Co,Ni and the topological insulators Bi2Te3 and Bi2Se3 using chemical state specific full hemisphere photoelectron diffraction and holography, STM, valence band and core level photoemission and DFT modeling as well. Our ab-initio calculations show that such hidden order at the interface leads to a suppression of the coupling between neighboring magnetic moments. The intact interface properties revealed by our experiments are suitable for devices based on spin-transfer torque effects between TIs and ferromagnetic layers.