If you want to compute reflectance and transmittance spectra for laterally structured samples you can use spectra of type 'Layer mix' instead of the type 'R,T,ATR'. With objects of this type you can average spectra of different layer stacks.

'Layer mix' spectra have a list of layer stacks rather than a single stack:

Press the Layer list button to open the list of the layer stacks used for this spectrum:

To add layers to this list drag&drop them from the list of layer stacks:

Each item in the list has a weight which should be proportional to the surface area that is covered by the corresponding layer stack. The sum of all weights should be 1.0 like in the following example:

For each layer stack in the list the spectrum is computed. The final spectrum is the sum of these 'sub-spectra' where each partial spectrum is multiplied by its weight factor.