This paper addresses the parts route selection and economic design in flexible manufactuirng system (FMS). Parts are processed through several stage workstations according to operation sequences. The machine of each workstation can do multiple operation functions. And the operation stage of a part can be processed in several workstations, which are non-identical in functional performance. The objective of this paper is to determine the processing routes of parts, number of machine at each workstation, number of vehicle and makespan time. Two models are suggested. One is assumed that the operation stage of parts can be processed at the only one among several available workstations. Other is assumed that the operation stage of parts is allowed to be processed at several workstations. Parts are transported by automated guided vehicles (AGVs). The decision criteria is to minimize the sum of processing cost, travel cost, setup cost and overhead cost. The formulation of models is represented. A solution algorithm is suggested, and a numerical example is shown.