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This paper studies the optimal inspection of autonomous robots in a complex pipeline system. We solve a 3-D region-guarding problem to suggest the necessary inspection spots. The proposed hierarchical integer linear programming optimization algorithm seeks the fewest spots necessary to cover the entire given 3-D region. Unlike most existing pipeline inspection systems that focus on designing mobility and control of the explore robots, this paper focuses on global planning of the thorough and automatic inspection of a complex environment. We demonstrate the efficacy of the computation framework using a simulated environment, where scanned pipelines and existing leaks, clogs, and deformation can be thoroughly detected by an autonomous prototype robot.