Mass-spring systems are of special interest for soft tissue modeling in surgical simulation due to their ease of implementation and real-time behavior. However, the parameter identification (masses, spring constants, mesh topology) still remains a challenge. In previous work, we proposed an approach based on the training of mass-spring systems according to known reference models. Our initial focus was the determination of mesh topology in 2D. In this paper, we extend the method to 3D. Furthermore, we introduce a new approach to simultaneously identify mesh topology and spring stiffness values. Linear elastic FEM deformation computations are used as reference. Additionally, our results show that uniform distributions of spring stiffness constants fails to simulate linear elastic deformations.