Rahman,
A couple of points to what you are trying to do.
- OptiFDTD is designed around propagation along the X or Z direction, which means your cross sections will need to be XY or ZY.
- The way materials are handled within OptiFDTD you would need to create a script that creates points of material at each grid point where the points are calculated to give the profile you want. This can take time but would give you what you want, have you worked with our scripting engine?