I just want to clarify what you are asking for as I am not certain. If you can answer the following questions I can better help with the problem.
1. Is this a 2D or 3D design?
2. It sounds like you want the waveguide cross-section in the xz plane and the propagation in the y-axis, is this correct?
3. Do you want your script changing the refractive index profile along the propagation length of the waveguide or to specify a complex cross-sectional profile?
4. Are you looking for regions of constant dielectric or is this special function you are using needed to produce a graded refractive index structure?
Scott