Optics question-vacuum chamber for Ellipsometry

I have shown a picture of our current ellipsometry setup. The sample is placed in the center. Polarized light comes in from the left barrel, reflects off the sample, and enters the barrel on the right. What I'm looking to build is a cover/chamber this that covers the sample but does not affect measurements to a great extent. The chamber is to enclose the sample in either a vacuum or inert gas environment. Obviously, two windows on the chamber have to be made in order for light to pass through and hit the sample. Visible light is used; normally we analyze data from 400nm upwards. Measurements are taken at a fixed angle (as shown in picture, 65 degrees).

I was hoping to double check my reason with some experts here before having this thing retrofitted. I do not deal with optics at all; after plowing through many textbooks and seeing how fertile the field is, I'm afraid that I'll overlook some physical phenomenon in designing this thing.

I feel that the factors that I need to be concerned about include polarization change as light passes through windows, refractive index, and transmittance. Is there anything else that needs to be considered? Is this problem as simple as building a chamber that has two windows at 65 degrees (normal to incident light to minimize refracted light) with a material that is offers close to 100% transmittance in the wavelength that I want?

Thank you very much for your input.
 
Below is the picture I promised.
 

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