This paper outlines opportunities and challenges in the implementation of BPEL based WFMS(WorkFlow Management System) for the MES(Manufacturing Execution Systems) in semiconductor manufacturing. At present, the most MESs in semiconductor wafer fabrication shop have the problems in terms of application software integration, reactivity, and adaptability. When a plant has to produce new product mix, remodel the manufacturing execution process, or replace obsolete equipments, the principal road blocks for responding to new manufacturing environment are the difficulties in porting existing application software to new configurations. In this paper, the issues about WFMS technologies including BPEL standard applied for MES are presented. And then, we introduce the integrated development framework named nanoFlow which is optimized for developing the BPEL based WFMS application for automated manufacturing system. And we describe a WFMS implemented with using nanoFlow framework, review and evaluate the system.