Sidewall roughness (SWR) of fluorinated polyether waveguides fabricated using reactive ion etching in pure oxygen gas was directly measured using atomic force microscopy (AFM). We confirm that SWR is not the replicate of line edge roughness (LER) of the waveguides. Statistical information such as standard deviation of roughness, autocovariance function (ACF), and autocorrelation length (ACL) have been obtained from AFM measurements. The ACL varies in the similar manner as SWR along the depth of the waveguide, and both are dependent on the etch depth. The depth dependence can be explained by the change in the arrival dynamics of etchant ions in a mechanism involving both shadowing and first-order reemission effects. (C) 2004 Elsevier B.V. All rights reserved.