This research addresses the problem of selecting the most appropriate Flexible Manufacturing System (FMS) for a manufacturing organization. A unified framework is proposed to facilitate decision making in the design and planning stage. The recommended framework contains three individual modules: an Analytic Hierarchy Process (AHP), a simulation module, and an accounting procedure. These modules are unified through an efficiency measurement method called Data Envelopment Analysis (DEA). The AHP model examines the nonmonetary criteria associated with corporate goals and long-term objectives, while the simulation model is employed to analyze the tangible benefits. Both AHP and simulation models are used to generate the necessary outputs for the DEA, whereas the accounting procedure determines the required inputs, such as expenditures and resources, for realizing the potential benefits. After solving an original DEA, a modification of the DEA structure is found to be imperative, because inappropriate multipliers (weights) are assigned by the conventional use of DEA and multiple efficient Decision Making Units (DMUs) are identified in the DEA solution. By applying weight flexibility restriction and cross efficiency methods to rectify the difficulty, this study finally identifies the most efficient FMS system.