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a b s t r a c tA numerical model was developed to simulate the nanoindentation of a Ni nanodot-patterned surface (NDPS) on a deformable Si substrate. Each contacting nanodot on the Si substrate was treated individually in this model and the interaction among the nanodots was considered through the elastic deformation of the Si substrate. The load-deformation relationship for the single-asperity contact between the indenter tip and a nanodot was determined using finite element analysis. A nanoindentation experiment on a Ni NDPS was performed to test the developed model. The simulation and experimental results were found to be in good agreement. The experimentally verified model was used to explore the effects of substrate deformation and surface roughness caused by the Ni nanodots on the nanoindentation behavior. It was found that the effect of the substrate and the effect of roughness must be considered. A detailed study of the substrate deformation shows that the interaction among nanodots, through the substrate, can contribute a considerable portion of the total deformation under a nanodot. The yield strength of the nanodot was found to have a significant effect on the contact deformation, while the elastic modulus was found to have little effect.