This paper analyzes surface chemistry effects to stably pattern aqueous two-phase system (ATPS) droplets on chemically modified poly(dimethylsiloxane) (PDMS). Polyethylene glycol (PEG) and dextran (DEX) are used as phase-forming polymers for the ATPS. PDMS surface modifications studied include primary amine groups, carboxylic acid groups, and neutral polymer surfaces. The PDMS surfaces were characterized by fluorescent measurement, water and DEX contact angle measurements, and X-ray photoelectron spectroscopy (XPS) analysis to confirm surface properties. While homogeneous surfaces of different functional groups affect DEX droplet pinning somewhat, the most stable patterns were realized using surfaces with chemical heterogeneity. Arbitrary DEX solution patterning was achieved on a chemically patchy surface.