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The development of autonomous systems requires a rigorous process that can guarantee a system’s reliability in critical applications. At its core, an autonomous system bases its behavior on a well-defined decision making system. In this paper, we present a methodological basis for the design, formalization and formal verification of Decision Making systems for autonomous agents. The approach is generally applicable to operational objectives that can be functionally decomposed and subsequently represented as Hierarchical Finite State Machines. As a case study, we present the application of this method to implement a Decision Making model in Simulink. Furthermore, we present how we use NASA’s FRET tool to write requirements in structured natural language and generate formal specifications that can be automatically digested by NASA’s CoCoSim tool. Finally, we present how, by leveraging CoCoSim, we perform formal verification against the Simulink model and present analysis results.