Soft lithography molding is a promising technique for patterning polymer integrated optical devices, however the presence of a background residue has the potential to limit the usefulness of this technique. We present the soft lithography technique for fabricating polymer waveguides. Several effects of the background residue are investigated numerically, including the modal properties of an individual waveguide, the coupling ratio of a directional coupler, and the radiation loss in a waveguide bend. Experimentally, the residue is found to be reduced through dilution of the core polymer solution. We find that the force with which the soft mold is depressed on the substrate does not appreciably affect the waveguide thickness or the residue thickness. Optical microscope images show that the residue is thinnest next to the waveguide. (C) 2004 American Vacuum Society.