This paper presents the novel method to control polymer surface morphology using reactive ion etching (RIE) technique and its application to microfluidic devices. By using this method, polymer surface morphology could be controlled in the wide range between smooth surface and grassy surface with a newly developed electron cyclotron resonance (ECR)-RIE system. It was found that the polymer surface morphology is closely related to metal micromask concentration on the surface. Our system could easily control the micromask concentration only by changing the total pressure in the chamber. The etching characteristics of 75 mol% O-2-CF4 gas mixture were systematically investigated as a function of total pressure. The smoothest surface with the arithmetic mean roughness value (R-a) 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 on the polymer surface under 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. (C) 2008 Elsevier B.V. All rights reserved.