A method of adhering a protective layer applied to a substrate region of an implantable medical device (IMD) to form a covered substrate region. The method includes obtaining the IMD, depositing an intermediate layer on a portion of the substrate region of the IMD such that the intermediate layer binds to the portion of the substrate region to create a modified substrate region, and depositing the protective layer after depositing the intermediate layer onto the intermediate layer and adhering the protective layer to the intermediate layer. In an embodiment of the present invention, this method enhances the sealing characteristics of the protective layer by, for example, reducing the likelihood of delamination of the protective layer from the IMD relative to IMDs prepared by certain other methods.