The purpose of this study was to develop a selective patterning process with functional nanoparticles, using the selective hydrophobic treatment which can give surface energy differences. It is important to selectively pattern the nanoparticles in solution, to the desired site in a variety of fields such as transparent electrodes, displays, and bio-sensors. Selective hydrophobic treatment can reduce the additional post processes such as cleaning to remove particles unwanted position, which is a drawback of the existing solution process. Various patterns with sub-micron size that can’t be achieved with other solution processes could be fabricated by nanoimprint lithography, selective surface treatment, and a solution coating process. The transparent conductive electrode (TCE) using silver mesh patterns on the flexible substrate created from our study showed 24 Ω of sheet resistance and more than 82% transmittance. To verify the possibility of nano-patterning of various materials, quantum dot (QD) was also patterned by selectively filling. Selective surface treatment technology has significantly improved the filling process of nanoparticles into fine patterns less than 1 μm wide.