Reactive (Ar-O2 plasma) magnetron sputtered WO3-MoO3 (nanometer scaled) mixed layers were investigated and mapped by Spectroscopic Ellipsometry (SE). The W- and Mo-targets were placed separately, and 30 × 30 cm glass substrates were slowly moved under the two (W and Mo) separated targets. We used different (oscillator- and Effective Medium Approximation, EMA-based) optical models to obtain the thickness and composition maps of the sample layer relatively quickly and in a cost-effective and contactless way. In addition, we used Rutherford Backscattering Spectrometry to check the SE results. Herein, we compare the “goodness” of different optical models depending upon the sample preparation conditions, for instance, the speed and cycle number of the substrate motion. Finally, we can choose between appropriate optical models (2-Tauc-Lorentz oscillator model vs. the Bruggeman Effective Medium Approximation, BEMA) depending on the process parameters. If one has more than one “molecular layer” in the “sublayers”, BEMA can be used. If one has an atomic mixture, the multiple oscillator model is better (more precise) for this type of layer structure.