The successful development of biosensors and protein chips requires a method for protein patterning on a solid surface. We describe a virtual mask photolithography method for the surface patterning of proteins on a chip using a micromirror array (MMA) and its characterization. The excitation light was switched on or off using the MMA, and the light pattern was transferred using the pattern of switched-on mirrors. The nitroveratryloxycarbonyl (NVOC) group was utilized as a photolabile protecting group for protein patterning, so that biomolecules could be immobilized on a patterned substrate. When illuminated by UV light, the photolabile protecting group was removed by a chemical reaction, and non-illuminated photolabile protecting groups protected the chip surface. Biotin was coupled only to the region where the protecting group had been removed, and so, biotin–streptavidin patterns were obtained. A two-dimensional MMA was designed and fabricated using micromachining technology for use as a spatial light modulator. The projection system consisted of the MMA, a light source and other optical components, such as a projection lens. Fluorescein isothiocyanate was used to visualize the NVOC photo-cleavage sites and the biotin–streptavidin reaction. Parallel and quantitative experiments required in the development of surface modification technology for protein immobilization on a surface can easily be performed using this protein patterning system.