The paper presents a systematic approach for stiffness modeling of manipulators with complex and hybrid structures using matrix structural analysis. In contrast to previous results, it is suitable for mixed architectures containing closed-loops, flexible links, rigid connections, passive and elastic joints with external loadings and preloadings. The proposed approach produces the Cartesian stiffness matrices in a semi-analytical manner. It presents the manipulator stiffness model as a set of conventional equations describing the link elasticities that are supplemented by a set of constraints describing connections between links. Its allows user straightforward aggregation of stiffness model equations avoiding traditional column/row merging procedures in the extended stiffness matrix. Advantages of this approach are illustrated by stiffness analysis of NaVaRo manipulator.