An optimization-based multilayer operability framework is introduced for the process design of nonlinear energy systems that are challenged by complexity and highly constrained environments. In the first layer of this framework, a mixed-integer linear programming (MILP)-based iterative algorithm considers the minimization of the footprint and the achievement of process intensification targets. Then, in the second layer, an operability analysis is performed to incorporate into the approach key features for optimality and feasibility, accounting for the system operation with changeable input conditions. The outcome of the framework consists of a set of modular designs, considering the aspects of both size and process operability. For this study, the nonlinear system is represented by multiple linearized models, resulting in low computational expense and efficient quantification of operability regions. The developed framework is applied to a membrane reactor for direct methane aromatization conversion to hyd...