The etching characteristics of polytetrafluoroethylene (PTFE) and perfluoroalkoxy (PFA) bulk plates were studied in a magnetron enhanced reactive ion etching (M-RIE) system. The etch rates of the plates for oxygen plasma were investigated under the pressure range 0.1-2.0 Pa, and were found to strongly correlate with the self-bias voltage. The plates presented smooth surface in the 0.1-1.0 Pa pressure range, and rough surfaces at 1.5 Pa and 2.0 Pa. The roughness was introduced by a micromask sputtered from the chamber material. The titanium etching mask exhibited lower etch rates for oxygen plasma than aluminum and silicon dioxide. Finally, using the dry-etched titanium mask in low-pressure oxygen plasma, we fabricated a 5-μm pitch line-and-space structure on a PTFE plate and a 4-μm square pillar array on a PFA plate.