Indium oxide doped with tin oxide, ITO, is extensively used to fabricate transparent conductive coatings. ITO thin film on flexible substrates has been used in applications including touch panel contacts, electrodes for LCD and Plasma displays. ITO thin film can be deposited onto polymer substrates using electron-beam evaporation. Surface modification of polymer substrate improves its superficial properties, adhesion in particular, to meet specific requirements while retaining the good mechanical properties of the substrates. In this study, a system consists of a linear ion beam and an electron beam which have been developed in vacuum. The linear ion beam treats the polymer surface while simultaneously the ITO thin film is deposited onto the surface using electron-beam evaporation. We demonstrated that polymer surface treated with the ion beam has been improved. Moreover, the linear ion beam source provides good uniformity of surface treatment and is very suitable for production-scale processes. An integrated electron-beam evaporation and linear ion beam system significantly increases the chemical compatibility of a polymer surface to an over-layer.