As a primary load-bearing component, stiffened shells are widely used in aerospace cabins, marine vessels, and other fields. Given the complex load situations of these structures, the traditional concept of periodic and uniform stiffening design no longer meets the standards of usage, and designing the stiffeners presents a challenging issue since both the deformation resistance and lightweight properties are highly demanded. In response to the above consideration, this paper proposes an integrated APDL-MATLAB topology optimization framework, with the former running the finite element analysis while the latter for the optimization and geometric control. The proposed method features in working on arbitrarily shaped structures that are discretized with any mesh type, addressing the issue of generally adopting the structured and uniformly-sized solid mesh. Compared to purely using a commercial topology optimization tool, the proposed framework can better distinguish between the shell domain and the stiffener domain, thus imposing design variations and geometric control only to the stiffeners. A few numerical examples will be presented to show the effectiveness of the proposed method.