Hydrophobic-hydrophilic patterns were formed on indium tin oxide substrates, and thick films of poly(phenylsilsesquioxane) (PhSiO3/2) particles, prepared by the sol-gel process, were selectively deposited onto hydrophilic areas of the substrates by electrophoresis. The films composed of PhSiO3/2 particles became transparent with morphological changes from aggregates of particles to a continuous phase after a heat treatment. After heat treatment at 200 °C, convex-shaped PhSiO3/2 micropatterns were formed on the hydrophilic region of the pattern. Moreover, the height of micropatterns was controlled by the deposition time. This patterning technique has a wide variety of applications such as fabrication of micro-optical components.