In this paper we propose a method to extract automatically metadata (title, authors, affiliation, email, references, etc) from science papers by combining the layout information of papers with rules which are defined by using JAPE Grammar rules of GATE. After metadata extracted automatically from digital documents, user can interact and correct them before they are exported to XML files. Developing a tool to extract metadata from digital documents is a very necessary and useful task for building collections, organizing and searching documents in digital libraries. The extraction method is tested on computer science paper collections selected from international journals, proceedings downloaded from digital libraries such as ACM, IEEE, Springer and CiteSeer.