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This paper demonstrates a flux/2-ethyl-1-hexanol mixture capable of performing a self-assembly process. An /Ar plasma treatment controls the surface free energy of Si, leading to better self-assembly driven by capillary force. Hydrophobic bonding pads resulting from ODT (1-octadecanethiol) SAMs (self-assembled monolayers) on a microchip can be self-assembled on hydrophobic bonding sites caused by a flux/2-ethyl-1-hexanol mixture on a substrate within 0.4 s. Microchips with 400200-rectangle bonding pads exhibited higher alignment precision (displacement error ; rotation error ) than 400400 -squares. The Owens-Wendt method was used to calculate the contact angle of 2-ethyl-1-hexanol to different bonding surfaces in water. Plasma treatment enabled the smallest contact angle of 2-ethyl-1-hexanol to ODT-modified Au surface (4.4), and the largest contact angle of 2-ethyl-1-hexanol to plasma-modified Si surface (153.5) in water. It explained why the plasma treatment exhibited benefit of self-assembly. This self-assembly technique could be used to assemble light emitting diodes, RFID tags, biosensors, or other types of microchips.