A method and system for scanning a set of documents is disclosed. The set of documents to be scanned are in an organizational format wherein groups of the documents are separated by barriers. The method and system include displaying a set of logical entities that represent the barriers to an operator of a scanner; and associating scanned images of the documents with at least one of the logical entities. The method and system further include using the association of the logical entities to store the scanned images, such that the organizational format of the documents is retained.