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The thickness characterization of transparent protective coatings on functional, transparent materials is often problematic. In this paper, a toolbox to determine the thicknesses of a transparent coating on functional window films is presented. The toolbox consists of a combination of secondary ion mass spectrometry and profilometry and can be transferred to other transparent polymeric materials. A coating was deposited on designed model samples, which were characterized with cross-sectional views in transmission and in scanning/transmission electron microscopy and ellipsometry. The toolbox was then used to assess the thicknesses of the protective coatings on the pilot-scale window films. This coating was synthesized using straightforward sol-gel alkoxide chemistry. The kinetics of the condensation are studied in order to obtain a precursor that allows fast drying and complete condensation after simple heat treatment. The shelf life of this precursor solution was investigated in order to verify its accordance to industrial requirements. Deposition was performed successfully at low temperatures below 100 °C, which makes deposition on polymeric foils possible. By using roll-to-roll coating, the findings of this paper are easily transferrable to industrial scale. The coating was tested for scratch resistance and adhesion. Values for the emissivity (ε) of the films were recorded to justify the use of the films obtained as infrared reflective window films. In this work, it is shown that the toolbox measures similar thicknesses to those measured by electron microscopy and can be used to set a required thickness for protective coatings. [ABSTRACT FROM AUTHOR]