A numerical model was developed to simulate the micro deformations of a polymeric substrate due to lithographic processing of different layers of a transistor-like structure. The results of the model were validated with the results from experiments. The model, a mechanical-thermal-hygroscopic model, takes into account the dimensional effects of temperature, moisture and stresses. It also includes the temperature dependent viscoelastic behaviour of the polymer substrate. The model can be used to predict overlay accuracies between different functional layers introduced by the lithographic process. It can also be used to understand the underlying processes such that it provides a tool to improve the overlay accuracy during actual processing.