Disclosed are systems to apply customized permission settings to protect particular regions of a document, and, in particular, documents that are of a lossy′ encoded media file type, e.g., an MPEG video format. The custom access permission settings may be implemented by obfuscating the protected regions of the original file and then embedding “secret,” e.g., hidden and/or encrypted, versions of the obfuscated regions in parts of the data structure of the original file, e.g., in the form of “layers” that are held within video stream containers. The content of the individual encrypted video stream containers may then be decrypted according to each recipient's permissions and layered on top of the obfuscated regions of the encoded media file before being displayed to the recipient. In some embodiments, additional layers of video may be used to reduce the appearance of aliasing around borders of the protected regions of the encoded media file.