This paper presents a navigation system for minimally invasive surgery, especially laparoscopic surgery in which operates in abdomen. Conventional navigation systems show virtual images by superimposing models of target tissues on real endoscopic images. Since soft tissues within the abdomen are deformed during the surgery, the navigation system needs to provide surgeons reliable information by deforming the models according to their biomechanical behavior. However, conventional navigation systems don't consider the tissue deformation during the surgery. We have been developing a new real-time FEM-based simulation for deforming a soft tissue model by using neural network. The network is called the neuroFEM. The incorporation of the neuroFEM into the navigation leads to improve the accuracy of the navigation system. In this paper, we propose a new navigation system with a framework of the neuroFEM.