Real time spectroscopy ellipsometry (RTSE) has been applied to study the evolution of thin film optical structure during sputter deposition of polycrystalline CdS/CdTe solar cell stacks on transparent conducting oxide (TCO) coated glass substrates optimized for high efficiency. RTSE provides information on (i) interface formation to the underlying high resistivity transparent (HRT) layer during initial CdS growth, (ii) bulk layer CdS growth and its surface roughness evolution, (iii) CdS/CdTe interface formation when the overlying CdTe layer is deposited on the CdS, and (iv) CdTe bulk layer growth and its roughness evolution. Structural/optical models developed in the analysis of RTSE data acquired at a single point are also applied in the analysis of ex situ mapping SE data obtained over the area of the completed solar cell stack. As a result, maps of the structural parameters can be extracted, which then can be correlated with maps of the small area device performance. When uncorrelated non-uniformities exist over the area, optimization by combinatorial methods is possible.