Beam Profile Through an Optical System I am curious about how to counteract the effect different optical elements have on a beam profile.  I know a good rule of thumb with lenses is that you should balance positive and negative ones to counteract aberrations.  I am wondering if anyone has any helpful tips on the effect polarizers, ND filters, beam splitters, ect., have and ways to balance out any effects they have on the beam profile.
 A: Assuming your flat optical elements are located in "infinity space" (i.e. the part of the optical system where a laser would be collimated), you don't have much to worry about in terms of spherical aberrations.  You might have color filtering effects depending on your optics, but there's not much to do about that if your optics are fixed. If you have flat optics at an angle (such as with a beamsplitting plate or dichroic mirror), you could introduce polarization filtering or beam shifts from refraction. Combating a beam shift is as easy as inserting another (transparent) plate tilted the other way to shift it back.
The main thing you do have to seriously consider, though, is reflections. In a microscope system, reflected light can scatter around and reduce the contrast of your images. Furthermore, transparent flat plates can act like poor Fabry-Perot cavities, giving you spurious interference fringing effects (such as oscillations in the detected spectrum). To minimize these, try to use anti-reflection coated optics, beam dumps, and wedged optics (like for windows) when necessary.  Good luck! 
