Currently, thin films are widely used for the display product. Furthermore, the protective film is often attached to touch films and cover glasses for their safety. However, relatively few researches have been done for those products and there are many issues when we use current inspection system for multi-layered thin films. In this paper, we propose the novel method to inspect them based on 3d surface reconstruction. We use line profiles of each layer which composes the multi-layered thin film. Also an enhanced light source system is applied to inspect user specified layers by using the patterned retarder. Also we propose the robust defect analysis system by using user specified depth images. We made 3d inspection platform which shows very stable results regarding defects detection among layers. Finally, our study is applied to the commercial system which is used for visual inspection of the film.