This paper describes the microfabrication of transparent thermoplastic plates, polymethyl-methacrylate, polycarbonate, and cyclic olefin polymer by an electron cyclotron resonance-reactive ion etching (ECR-RIE) system. The system was adopted for the microstructure with smooth surface and high-aspect ratio. The etching was carried out using O2/CF4 plasma. The etching conditions are set at 13.56 MHz high-frequency output of 100 W (self-bias voltage: -430 V--310 V) and the stage temperature of -15°C. We have examined the surface roughness and the optical properties at the range of process pressure 0.05-0.5 Pa. The surface roughness of etched substrates is below 20 nm and the average transmittance is over 98% at the process pressure of 0.05 Pa.