A method for separating and categorizing documents includes receiving a scanned batch of documents. The batch includes scanned documents to which document separator stamps have been applied before scanning. Each stamp includes machine recognizable patterns applied on a same page of a document, spaced by a designated field for receiving a user-applied category code. The scanned batch of documents is processed to identify pages that contain a document separator, including identifying at least one of two spaced patterns. For a document page for which a document separator is identified, the the corresponding designated field is located and the category code associated with the designated field identified. The document containing the is separated from other documents in the batch based the identified separator and a document category is assigned to the document, based on the identified category code.