The interfacial interaction of 2D materials with the substrate leads to striking surface faceting affecting its electronic properties. Here, we quantitatively study the orientation-dependent facet topographies observed on the catalyst under graphene using electron backscatter diffraction and atomic force microscopy. The original flat catalyst surface transforms into two facets: a low-energy low-index surface, e.g. (111), and a vicinal (high-index) surface. The critical role of graphene strain, besides anisotropic interfacial energy, in forming the observed topographies is revealed by molecular simulations. These insights are applicable to other 2D/3D heterostructures.

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