A metadirectory namespace is provided for storing files and directories "hidden" from one or more user-accessible namespaces. The metadirectory namespace is a separate, parallel namespace that coexists with other user-accessible namespaces in a storage operating system. Files and directories may be identified as being stored in a metadirectory based on their location or based on their associated flags. The metadirectory namespace may be selectively exported only to clients, users and applications given special file access permissions.