A system and method for storing computer files in a destination file is described, which may be an incremental backup system. File headers related to the files may be stored in a file index separate from a data file, or subsequent versions may be stored in the same data file while maintaining earlier versions. File headers may include locations of files, checksums, metadata about individual blocks corresponding to the data files. A system may include a client application program stored on a client computer, a network, and a server software program on a destination computer. Embodiments may include compression, encryption, or both, performed by the client application program. Files may be divided into blocks, and metadata may include locations of blocks. Files may be restored from the destination computer to the source computer.