In principle any geometric shape can be handled by Nazca. I don’t know how practical that will be for studying the roughness roughness in waveguides. There is not a specific functionality implemented for this.
There is literature on this which might provide a useful solution to your problem, e.g. Melati et al. “A unified approach for radiative losses and backscattering in optical waveguides”, J. of Optics, Vol. 16, 5, 2014.