The analysis of thin layers in semiconductor components represents a central point in the quality control of semiconductor companies. Not only to control production processes, but to successfully operate also reverse engineering, reliable thin-film measurement methods are essential. In this work, non-destructive thin film EDX (energy dispersive X-ray micro analysis) software and μXRF (micro x-ray fluorescence analysis) were compared with TEM analysis. These methods ensure a high lateral resolution which is essential in the analysis of semiconductor structures. As an example, four different, for the semiconductor industry interesting, very thin coating systems in the nanometer range have been tested. In the individual cases best TEM detector contrast settings could be found, as well as optimum fluorescence lines settings on the EDX to minimize the errors. The TEM measurements, in thickness and composition, were compared to the thin film EDX software and the μXRF method results to determine their accuracy. It turns out that depending on the layer system recalibration with multilayer standards or at least with elemental standards is recommended. It could be shown that with μXRF and thin film EDX a reliable, rapid and non-destructive layer analysis is possible.