An anisotropic etching process of a perfluorocyclobutene polymer that makes use of a spin-coated photoresist mask instead of a commonly used thin metal layer is reported. We demonstrate that such masking can be applied to advantage for anisotropic reactive ion etching of polymers if the wafer is cooled down to T = -50 degrees C. For the fabrication of integrated optical waveguides, the choice of an appropriate photoresist is very important if the edge roughness needs to be low in order to avoid optical scattering losses. For such applications, the Microresist Technology ma-P 1275 has been found to be very suitable.