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A novel supercritical fluid deposition method (SCFD) of SiO2 has been developed for polymer-based MEMS. In order to reduce deposition temperature for the application to polymer-based MEMS process, we selected O3 as an oxidant in SiO2-SCFD. Conformal SiO2 deposition on Si trenches (aspect ratio 24) at low temperatures (below 200°C) was achieved, which were acceptable for deposition on polymers. In addition, SiO2 coating on inner wall surface of microchannels, which was made of polydimethylsiloxane (PDMS), was demonstrated.