There is tab available on the top of CST main window which will calculate Q and losses for you.
Be sure to define proper material for model.
I am not able to understand your problem correctly as from question it seems that you want to do something to note the effect of change of aperture of waveguide if you explain a bit more then it would be easy to answer. But I think you want to see the insertion loss of waveguide for a particular aperture on certain frequency range. If it is the problem then you can very easily do it it with S parameter solver of CST by proper definition of ports