Microfluidics is an emerging technology that has gained attention by the industry for its capabilities to investigate and visualize fundamental recovery mechanisms at the pore scale in a microdevice, mimicking, to some extent, the actual rock pore-network. While current technologies are capable of building micromodels that are either water-wet or oil-wet, a technique to achieve a representative mixed-wet property is still unreached. In this work, we introduce a novel surface coating capability using thin film deposition to fabricate surfaces with selective wettability, oil-wet and water-wet, an effort to mimic actual mixed-wet rock. This unique approach enables the generation of hydrophobic surfaces in selected regions by altering the hydrophilic surface property of silicon substrate at the microscale. A selective wettability control mask and Perfluorodecyltrichlorosilane (FDTS) hydrophobic coating using molecular vapor deposition (MVD) were used for surface wetting properties alteration. Surface measurements, including contact angle measurements, X-ray photoelectron spectroscopy (XPS), and Transmission Electron Spectroscopy (TEM) imagining, were performed to evaluate the thin-film composition and morphology. By altering the wetting state of the substrate by the coated film, a selective mixed wettability surface was achieved. This technique has the potential to be utilized in microfluidic device developments. Tuning the wetting state of the substrate to mimic the mixed-wet characteristics of reservoir rocks, such as carbonates and shales, can enhance our understanding of complex fluid behaviors in porous media and provide a crucial contribution to many subsurface petroleum engineering applications such as enhanced oil recovery (EOR) and CO2 storage.