Rather vague question!
by the way when you calculate S11 on a waveguide port you mean the ratio of the outgoing power to the incomming power at that port in a certain mode.
If you use an incident (lets suppose) plane wave on an structure and want to know the ratio of the reflected plane wave (here plane wave is the ceratin mode) to the incident one, you are actually measuring "Radar Cross Secition"
simply HFSS has got this output and you may evaluate it.
Do you want to irradiate the structure with a plane wave?