Roll-to-Roll systems handling web material such as papers, polymers, textiles or metals are very common in the industry. Printing, coating and drying are examples of operations that can be performed in different sections of a web line. In Roll-to-Roll systems, troughs and wrinkles of the web are the most common and the most expensive defects. In addition, these are difficult to detect and it is even more difficult to understand their origins. In fact, troughs and wrinkles can come from a misaligned roller, a lateral guide, temperature and moisture variations, web/roller friction, non-uniform web tension, etc. It is therefore relevant for industrial production lines to simulate the dynamic 3D behavior of the moving web, by using finite element modeling. This presentation focuses on finite element modeling and analysis of moving flexible webs in Roll-to-Roll systems in order to understand which parameters lead to web wrinkles and which are the most influent.