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We demonstrate ordered array formation of Au nanoparticles by controlled solid-state dewetting of a metal film on stepped alumina substrates. In situ transmission electron microscopy studies reveal that the dewetting process starts with nucleation of ordered dry regions on the substrate. The chemical potential difference between concave and convex surface regions induces anisotropic metal diffusion leading to the formation of nanowires in the valleys. The nanowires fragment due to Rayleigh instability forming arrays of metal nanoparticles on the substrate. The length scale of reconstruction relative to the starting film thickness is an important parameter in controlling the spatial order of the nanoparticles.