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The presence of nanobubblesas imaged with tapping-mode atomic force microscopyis controlled using nanopatterned surfaces possessing repeating patterns of polystyrene (hydrophobic domains) and poly(methyl methacrylate) (hydrophilic domains). For nanobubbles to be present, we find that, in addition to controlling the degree of surface hydrophobicity, it is important for the spatial dimensions of the hydrophobic domains on the nanopatterned surface to be commensurate with the equilibrium topology of the nanobubbles.