Hi Michael,
Perhaps micro/macro was not the best way to describe it. What FDTD can do is model the bulk properties of a material through the complex refractive index (n_complex = n – jk). If you can model your material in this fashion then OptiFDTD can do so. This would of course only model the absorption. Scattering is from the micro structure which you are correct would be difficult to directly model.
The other concern I have is that you are looking to model structures centimeter in scale. A finite-difference time-domain solution requires a resolution with a maximum size of roughly lambda/10 (often much smaller) for numerical stability. This could lead to a very computationally intensive calculation. What wavelength are you operating at?
Scott