Virtual enterprise or e-manufacturing is an advanced and effective manufacturing mode to modern manufacturing enterprises. In these modes, business process has been extended to outer enterprises, i.e. inter organization workflow. In order to achieve a efficient tool for workflow modeling with both simplicity and semantics, matter element is applied to construct a matter element digraph, in which a node is matter element. Then manufacturing service based workflow model can be dynamically changed or composed by matter element transformation. A case is studied to explain the approach presented in this paper.