In this study we report new results on the changes in optical properties of glass surfaces induced during wet photolithography using Oblique Incidence Reflectivity Difference Ellipsometry (OI-RD). A novel wet UV-photolithographic method for patterning phospholipid bilayers into two-dimensional arrays of voids and patches on hydrophilic glass substrates is presented. Especially, this technique involves etching the glass substrate fused with lipid vesicle solution and subsequently illuminated with short-wavelength UV light through a photo mask thus creating voids in the irradiated regions. The effects of the chemical etching and subsequent UV irradiation on the surfaces of microscope glass slides are investigated using the OI-RD technique. In this study, we have observed that the UV irradiation after chemical etching further changes the properties of the surface, even in the absence of the lipid bilayer. As a result, irradiating the chemically etched surface before the UV photolithography step renders the whole surface homogenous. Furthermore, fluorescence recovery after photobleaching (FRAP) experiments have been conducted on such homogenized surfaces which reveal that the fluidic properties of the membranes are retained. The created patterns are suitable to study protein-DNA interactions in the lipid environment. Our long term goal is to utilize this technique as a new screening approach for testing drug interactions above and below the cell surface.