Sidewall roughness (SWR) of fluorinated polyether waveguides fabricated using reactive ion etching was directly measured using atomic force microscopy. We confirmed the pressure dependence of SWR for shallow structures and discovered an additional etch depth dependence for deeper structures which counteracts the pressure dependence. Lower O2 pressure etching produces SWR which increases with depth while higher O2 pressure etching produces declining SWR with depth. Addition of N2 to the etch ambient suppresses SWR for high pressure etches at intermediate depths. The role of N2 is possibly related to the formation of a N-containing passivating film, confirmed by secondary ion mass spectroscopy measurements.
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