We present a thiol-ene/methacrylate-based photopolymer capable of creating coplanar physical features (e.g. micro-fluidic channels) and optical index features (e.g. waveguides) using standard mask-based lithography techniques. This new photopolymer consists of two monomer species that polymerize at different rates. By selectively exposing different areas of a device for various amounts of time, we can select the state of the polymer (i.e. liquid, rubbery, or glassy) to create fluid channels or optical index structures such as waveguides. Using only three exposure steps and two masks, we demonstrate an integrated refractometer with a 90° channelwaveguide crossing to illustrate the fabrication process and the ability to create lithographically aligned waveguides across a gap.