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This paper shows three-dimensional micro-scale self-assembly using hydrophobic interaction. We fabricated micro-scale particles (10×10×5 μm) and modified the wettabilities of the surfaces by forming self-assembled monolayers (SAMs). In 2-isopropanol (IPA) solution, the particles were stirred and self-assembled. The hydrophobic interaction acts on the two hydrophobic surfaces of the particles. The selectivity of the bindings was examined by counting the number of the bound particles. We showed the hydrophobic interaction can be applied to the micro-scale self-assembly.