Ex-situ spectroscopic ellipsometry (SE) has been advanced for the determination of the optical structure of CdTe solar cells on transparent conducting oxide (TCO) coated glass superstrates. SE measurements directly through the top glass are performed using a method in which the reflection from the glass/film-stack interface is collected whereas the reflection from the ambient/glass interface is blocked. The approach applies reference dielectric functions for the CdS and CdTe deduced from real time SE and for the TCO components from the coated glass before solar cell fabrication. A step-by-step fitting procedure identifies the most important thicknesses and compositional parameters for optimum methodology of characterization. This methodology has potential applications for quantum efficiency predictions, large area mapping, and on-line monitoring. SIMS analysis has been performed in an attempt to corroborate step-by-step analysis of through-the-glass SE data. SIMS and SE are in reasonable accord, and this supports SE as a viable non-invasive method for solar cell analysis at a single point or in a mapping mode.