A deduplication storage system and a backup application create a synthetic backup. Metadata instructions are provided to the deduplication storage system. Each of the metadata instructions specifies the data segment of an originating backup and a designated location of the data segment in the synthetic backup. Each of the metadata instructions are processed by locating those data sub-segments in the deduplication storage system specified by the data segment in each of the metadata instructions, and creating metadata references to each of the data sub-segments and adding the metadata references to metadata of the synthetic backup being created.