In spectroscopic ellipsometry (SE) measurements of thin films with inhomogeneous optical thickness, the spot size of the probe beam on the sample surface is a highly critical parameter in the treatment of the experimental data. SE measurements were performed on transparent samples prepared by various techniques : plasma enhanced chemical vapor deposition of diamond film, spin-coated PMMA films and thermally grown SiO2 film. The first two deposition techniques can produce films with inhomogeneous optical thickness. By comparing SE measurements using different set-up configurations, we demonstrate that a combination of lenses and small diaphragms is most suitable for minimizing the effects related to the optical thickness distribution and light beam divergence. In this way mistakes are avoided in extracting physical parameters from SE optical modeling of these films.