We examine the effects of surface preparation and window birefringence on the determination of Cd965Zn035Te temperatures, prior to the deposition of Hg1-xCdxTe alloys by molecular beam epitaxy. We find that the different surface morphologies and chemical statuses induced by the substrate preparation recipe are responsible for the large run-to-run changes in the measured temperature. We speculate on the nature of the overlayers produced on the sample surface and obtain the optical constants of Hg chemisorbed on the Te-rich CdZnTe surface. We also investigate the possibility of using a critical point model for the CZT dielectric function in order to decrease the sensitivity of spectroscopic ellipsometry to the presence of overlayers. We prove by a simulation that an instrument capable of measuring at least 400 wavelengths in the range between 2.5 and 4.0 eV is needed to achieve good results with this method. Such instruments are available. Finally, we find that variations in window birefringence due to window baking occur in our system and can be detrimental to the run-to-run accuracy if not taken into account. (C) 2002 Published by Elsevier Science B.V.