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Over the past decades, the design and development of mission based Autonomous Underwater Vehicle (AUV) continues to challenge researchers. Although AUV technology has matured and commercial systems have appeared in the market, a generic yet robust AUV command and control (C2) system still remains a key research area. This paper presents a command and control system architecture for modular AUVs. We particularly focus on the design and development of a generic control and software architecture for a single modular AUV while allowing natural extensions to multi-vehicle scenarios. This proposed C2 system has a hybrid modular-hierarchical control architecture. It adopts top-down approach in mission level decision making and task planning while utilizing bottom-up approach for navigational control, obstacle avoidance and vehicle fault detection. Each level consists of one or more autonomous agent components handling different C2 tasks. This structure provides the vehicle developers with an explicit view of the clearly defined control responsibilities at different level of control hierarchy. The resultant C2 system is currently operational on the STARFISH AUV built at the ARL of the National University of Singapore. It has successfully executed some autonomous missions during sea trials carried out around the Singapore coastal area.