During the manufacturing of printed electronic circuits, different layers of coatings are applied successively on a substrate. The correct thickness of such layers is essential for guaranteeing the electronic behavior of the final product and must therefore be controlled thoroughly. This paper presents a model for measuring two-layer systems through thin film reflectometry (TFR). The model considers irregular interfaces and distortions introduced by the setup and the vertical vibration movements caused by the production process. The results show that the introduction of these latter variables is indispensable to obtain correct thickness values. The proposed approach is applied to a typical configuration of polymer electronics on transparent and non-transparent substrates. We compare our results to those obtained using a profilometer. The high degree of agreement between both measurements validates the model and suggests that the proposed measurement method can be used in industrial applications requiring fast and non-contact inspection of two-layer systems. Moreover, this approach can be used for other kinds of materials with known optical parameters.