Localized modification of the surface chemistry of microchannels broadens the spectrum of processes conducted at a microscopic level and permits the integration of several processes into a single continuous one. Due to the different types of materials used in fabrication microchannels and in modifying the surface chemistry, the selective patterning of a microchannel becomes challenging due to the need of patterning techniques compatible with the materials used for fabrication and modification and due to the required precision of the patterns. Herein, we propose the development of novel selective patterning techniques for two classes of substrates bonded to polydimethylsiloxane (PDMS) microchannels, namely polymer-and silicon-based substrates, with surface chemistry tunable nanoporous materials. The techniques are based on surface functionalization and on ex- and in-situ crystal growth of both functionally tuned porous materials. The performance of the selectively patterned devices will be verified for liquid-liquid phase separation and enhanced in-droplet mixing in microfluidic devices.