@Jeffrey.Strecker 

In general, I see the Clear Aperture as “where the rays are intended to pass”. But what happens to the rays that fall outside the Clear Aperture is unclear. They could be absorbed, reflected, ...etc. This is why you don’t automatically get the behaviour you expect.

One thing you can do, is change the Face Coat/Scatter properties. In the Object Viewer, you can see that the Side Faces have an ID of 0 (look at the top-left corner):

In the Object Properties, under the Coat/Scatter tab you can change Face 0, Side Faces Is Absorbing:

OpticStudio will then terminate the rays that fall outside the Clear Aperture:

I hope this helps and take care,

David