A data storage and protection system includes secondary storage and at least one instance of a high efficiency storage application (“HESA”). The HESA backs up and archives client data stored in primary storage of a client computer system or client node to secondary storage. Archive files generated by the HESA re-use previously backed up client data stored in the secondary storage. In one embodiment, previously backed up client data is re-used for an archive file by organizing the archive file as a hash tree having hash values pointing to the previously backed up client data. In addition, the HESA can maximize available space in the primary storage by replacing previously backed up and/or archived client data in the primary storage with pointers that point to the previously backed up and/or archived client data in secondary storage.