In order to calculate deformation of soft tissue under arbitrary loading conditions, we have to take both non-linear material characteristics and subcutaneous structures into considerations. The estimation method of material properties presented in this paper accounts for these issues. It employs a compression test inside MRI in order to visualize deformation of hypodermic layered structure of living tissue, and an FE model of the compressed tissue in which non-linear material model is assigned. The FE analysis is iterated with updated material constant until the difference between the displacement field observed from MR images and calculated by FEM is minimized. The presented method has been applied to a 3-layered silicon rubber phantom. The results show the excellent performance of our method. The accuracy of the estimation is better than 15 %, and the reproducibility of the deformation is better than 0.4 mm even for an FE analysis with different boundary condition.