A Reconfigurable Manufacturing System (RMS) is an intelligent and advanced manufacturing system capable of adapting its functionality and production capacity to market demand through configuration adjustments or the addition of new components. The primary objective of an RMS is to achieve an optimal economic cost over its entire life cycle. Therefore, studying system configuration and technology in order to economically evaluate costs and reduce total production costs while maintaining quality, as well as implementing RMS technologies at different system levels, is of great importance. The aim of this paper is to present a systematic design of the structural model of an RMS to illustrate its configuration status and to evaluate its quantitative, qualitative, and ultimately economic characteristics. Various RMS configuration models are introduced, and the efficiency and performance of the proposed model are analyzed from the perspectives of reliability, convertibility, quality, productivity, and material flow rate using systems engineering theories, Boolean algebra, and related approaches. A mathematical model is developed to estimate system productivity. In addition, a product cost model and an investment cost evaluation model based on Real Options Theory are presented and examined through a case study.