I have an optical system composed of a laser with only TE input, one collimation lens, one isolator and one focusing lens. Due to the fact that the isolator is tilted and has multiple un-coated internal interfaces which introduced some Fresnel loss, if I use polarization in POP, I got about 15% lower coupling efficiency into my fiber comparing with not use polarization. But I want to account for the AR coatings on the lens surface and isolator front and back surface, in this case, how do I define the polarization in the system explorer and the POP to get an accurate result?

Thanks for your advice.