This paper presents the use of a topological model to simulate a soft body deformation based on a Mass-Spring System. We provide a generic framework which can integrate any kind of geometrical meshes (hexahedral or tetra- hedral elements), using several numerical integration schemes (Euler semi-implicit or implicit). This framework naturally allows topological changes in the simulated object during the animation. Our model is based on the 3D Linear Cell Complex topological model (itself based on a 3D combinatorial map), adding the extra information required for simulation purposes. Moreover, we present some adaptations performed on this data structure to fit our simulation requirements, and to allow efficient cutting or piercing in a 3D object.