A computer implemented method, apparatus, and computer program product for using a virtual file system to encrypt files. The process registers a plurality of file systems on a data processing system with the virtual file system. The virtual file system is enabled to encrypt files without intervention from any file system in the plurality of file systems. The virtual file system identifies whether a file on a given file system is an encrypted file using a map file associated with the given file system. In response to identifying the file as an encrypted file, the virtual file system encrypts all data written to the file in accordance with encryption specifications in the map file.