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A systematic topology optimization based approach is proposed to design the optimal stiffener of three-dimensional shell/plate structures for static and eigenvalue problems. Optimal stiffener design involves the determination of the best location and orientation. In this paper, the stiffener location problem is solved by a microstructure-based design domain method and the orientation problem is modelled as an optimization orientation problem of equivalent orthotropic materials, which is solved by a newly developed energy-based method. Examples are presented to demonstrate the application of the proposed approach.