The purpose of this study is the development of an optimization model to design a coal bed methane (CBM) gas separation system using a multi stage membrane process. The proposed model is formulated using a nonlinear programming (NLP) technique and includes maximizing the total profit as the objective function, along with several constraints to fulfill the design specification under various scenarios. Using the proposed model, we can (i) identify the optimal system configuration and operation strategies such as the required membrane area, the number of stages, recycle strategies, and utility consumption; and (ii) analyze the cost contribution and major cost drivers that have effects on the system configuration and economics. We also investigate the sensitivity of major parameters, including the composition of the raw CBM feed and CH4 market price on the process configurations and operation strategies that affect the overall economics of the CBM production system.