During the expected lifetime, evolving economical and optimum reconfigurable manufacturing system (RMS) configuration in a desired period to give the exact functionality and the exact capacity needed, when it is needed, is an important optimisation problem. This paper presents RMS configuration design methodology in a desired period with optimisation of the present worth of total cost of RMS including capital cost of machine investment, reconfiguration costs, operating costs, maintenance costs and salvage value over time. The configuration decision considers flow line features such as multi-product, number of stages, and functionality blocks in each stage, etc., with various constraints satisfaction. Phase 1 aims at RMS evolution scenario and the mathematical modelling. Phase 2 evolves RMS configuration alternatives. Phase 3 aims at RMS configuration alternative optimisation using mathematical model and artificial immune system. A case study demonstrates the methodology, the effectiveness of the methodology and also some superiority of the proposed methodology compared to existing approaches.