I think we can calculate the coupling efficiency by placing two monitors like one will be placed on the structures or after the source (if you have any waveguide structure) and another monitor will be placed on top of the structure after the end of the structure (where the collection optics will be placed in the experiment, by considering the dimension of the monitor and the distance to get a rough idea of the numerical aperture(NA)), by calculating the transmitted power ratio you can get the coupling efficiency. 

Anyway, this is applicable to the cylindrical waveguide structure. you can share your structure to get more understanding.