The data storage system according to certain aspects can filter secondary copies of data (e.g., backups, snapshots, archives, etc.) generated by multiple client computing devices into a single, filtered, global reference copy. A reference copy may be a filtered view or representation of secondary storage data in a data storage system. A reference copy may include a data structure that includes references to a subset of secondary storage data that meets certain filtering criteria. The filtering criteria may be specified by users according to user preference. Data included in a reference copy may be stored in native format (e.g., format of the application that generated the data) and be accessible through the application associated with the data.