In soft tissue surgery, a tumor and other anatomical structures are usually located using the preoperative CT or MR images. However, due to the deformation of the concerned tissues, this information suffers from inaccuracy when employed directly during the surgery. In order to account for these deformations in the planning process, the use of a bio-mechanical model of the tissues is needed. Such models are often designed using the finite element method (FEM), which is, however, computationally expensive, in particular when a high accuracy of the simulation is required. In our work, we propose to use a smoothed finite element method (S-FEM) in the context of modeling of the soft tissue deformation. This numerical technique has been introduced recently to overcome the overly stiff behavior of the standard FEM and to improve the solution accuracy and the convergence rate in solid mechanics problems. In this paper, a face-based smoothed finite element method (FS-FEM) using 4-node tetrahedral elements is presented. We show that in some cases, the method allows for reducing the number of degrees of freedom, while preserving the accuracy of the discretization. The method is evaluated on a simulation of a cantilever beam loaded at the free end and on a simulation of a 3D cube under traction and compression forces. Further, it is applied to the simulation of the brain shift and of the kidney’s deformation. The results demonstrate that the method outperforms the standard FEM in a bending scenario and that has similar accuracy as the standard FEM in the simulations of the brain-shift and of the kidney’s deformation.