A virtualized application runs on top of a guest operating system (OS) of a virtual machine and is supported by a file system of the guest OS. The method of supporting the virtualized application with the file system includes provisioning a first virtual disk as a data store of the file system and a second virtual disk for the virtualized application, wherein the first and second virtual disks store first and second files of the virtualized application, respectively, retrieving metadata of the virtualized application, updating a master file table of the file system according to the retrieved metadata to map the first files to logical blocks of the file system, updating the master file table to map the second files to additional logical blocks according to the retrieved metadata, and creating a mapping for the additional logical blocks, that is used during an input/output operation, according to the retrieved metadata.