This article demonstrates the novel approach of fabricating molecularly imprinted polymers (MIPs) as fiber optic waveguides for the detection of fluorescent analytes. Combining a polyurethane system and the soft lithography technique of micromolding in capillaries (MIMIC), polymer waveguides of 50 νm and 100 νm dimensions were patterned onto a silicon substrate. Laser coupling into small waveguide segments has been verified visually. Binding experiments using the waveguides are currently being explored. Some preliminary binding studies have been performed, however, for smaller, freestanding filaments of sizes consistent with conventionally prepared MIP particles. Using fluorimetry measurements, templated fibers of 20 νm dimension preferentially bound the analyte molecules by a factor of 1.5 as compared to control polymers.