This paper presents the novel method to control polymer surface morphology using Reactive Ion Etching (RIE) technique and its application to microfluidic devices. This method controls surface morphology in wide range between smooth surface and grassy surface by a newly developed Electron Cyclotron Resonance (ECR)-RIE system. The etching characteristics of 75mol%O2-CF 4 gas mixture were systematically investigated as a function of pressure. The smoothest surface with the roughness (Ra) less than 10 nm was achieved at 0.1 Pa. On the other hand, the grassy surface with high aspect ratio of 80 was uniformly formed in the higher-pressure range from 1.0 Pa to 1.5 Pa. Furthermore, the proposed method was applied to microfluidic channels with multiple pillars, and a hybrid structure with smooth and grassy surfaces. ©2007 IEEE.