Patterning proteins at the sub-micron and nanoscale has many uses, including fabrication of protein arrays for diagnostic and sensor applications. Many groups have reported micron scale protein patterns using photolithography; however, smaller scales have not been realized. In this study, we demonstrate sub-micron protein patterns using photolithography. Patterning is achieved by chemical transformation of pH-reactive polymer films. Site-specific immobilization of streptavidin within a protein resistant background is demonstrated. This methodology could be utilized for the development of high density proteins arrays for biotechnology applications.