An element of a file system is virtually deleted by creating a deletion marker for the element. Two or more separate physical file system directories are presented as one merged (virtual) file system directory to a process running in a silo. The operating system provides the merged view of the file system directories by monitoring file system requests made by processes in silos on a computer or computer system and filtering out those elements associated with deletion markers. Special processing is invoked in response to detecting certain types of file system access requests, including: enumeration, open, create, rename or delete.