In order to achieve patterned surfaces for microfluidic applications, we show for the first time the use of self-assembled monolayer (SAM) of Hydroxy-phenyl porphyrin on SiO2 surface following a chemical procedure. The SAM was characterized using ground state UV-absorption spectroscopy and H2O contact angle measurements. The UV-absorption spectra of the SAM exhibited a ∼ 8 nm red shift in the Soret band compared to the porphyrin in toluene. This indicated the side-by-side orientation of the self assembled porphyrin molecules on SiO2. The molecular self-assembly is expected to be randomly oriented because of amorphous nature of the substrate. Sessile deionized (DI) water drop of 50 μL on SAM exhibited a contact angle of 75±3° which is significantly higher than the contact angle of 33±2° measured on the SiO2 substrate. In this paper, we also demonstrate an approach of patterning the SiO2 surface with the porphyrin SAM in order to achieve alternate hydrophobic/hydrophilic surfaces on a p-type device-quality (111) Si wafer. The application of such patterned surfaces is demonstrated with the help of microfluidic simulations study. A three-dimensional numerical simulation of flow in patterned microchannels with alternate layers of hydrophilic and hydrophobic surfaces at the bottom wall is studied here. Volume of fluid method (VOF) is used for simulating the free surface flow in the microchannel. Non-symmetric meniscus profiles with varying amplitude and shapes are obtained by changing the contact angles of the hydrophilic and hydrophobic surfaces. Flow instability is found to increase in the microchannels with patterned surfaces containing a variation in contact angles. © 2007 IEEE.