Permanent magnet machines with segmented stator cores are affected by additional harmonic components of the cogging torque which cannot be minimized by conventional methods adopted for one-piece stator machines. In this study, a novel approach is proposed to minimize the cogging torque of such machines. This approach is based on the design of multiple independent shapes of the tooth tips through a topological optimization. Theoretical studies define a design formula that allows to choose the number of independent shapes to be designed, based on the number of stator core segments. Moreover, a computationally-efficient heuristic approach based on genetic algorithms and artificial neural network-based surrogate models solves the topological optimization and finds the optimal tooth tips shapes. Simulation studies with the finite element method validates the design formula and the effectiveness of the proposed method in suppressing the additional harmonic components. Moreover, a comparison with a conventional heuristic approach based on a genetic algorithm directly coupled to finite element analysis assesses the superiority of the proposed approach. Finally, a sensitivity analysis on assembling and manufacturing tolerances proves the robustness of the proposed design method.