This paper addresses the processing route of parts and economic design in flexible manufacturing systems (FMSs) employing AGVs for Transport. Parts are processed through several workstations according to operation sequences. The machine of each workstation can do multiple operation functions. 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 route of parts, number of machines at each workstation, number of vehicles. The model is assumed that the operation stage of parts can be processed at the only one among several available workstations. Parts are transported by automated guided vehicle system(AGVS). The decision criteria is to minimize the sum of processing cost, travel cost, operating cost. A model formulation is represented. A solution algorithm is suggested by using mathematical programming and simulation technique, and a numerical example is shown.