In this paper we propose a method to address the problem of non-rigid registration in real-time. We use Lagrange multipliers and soft sliding constraints to combine data acquired from dynamic image sequence and a biomechanical model of the structure of interest. The biomechanical model plays a role of regulariza- tion to improve the robustness and the flexibility of the registration. We apply our method to a pre-operative 3D CT Scan of a porcine liver that is registered to a se- quence of 2D dynamic MRI slices during the respiratory motion. The finite ele- ment simulation provides a full 3D representation (including heterogeneities such as vessels,tumor,. . . ) of the anatomical structure in real-time.