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The use of preferential etching and atomic force microscopy to measure refractive index profiles of optical fibers is investigated. Both the etch rate and the position of lateral features are shown to be independent of etch time. An elliptical core fiber was studied and the resultant profile was found to be in qualitative agreement with the preform index profile. It is shown, however, that the ellipticity of the core has changed during the drawing process. The method was extended to fluorine and germanium doped planar waveguides and the results correlated with the fabrication process. © 1997 American Institute of Physics.