This paper presents a numerical method to construct a finite element model of a disorder in skeletal system by deforming a finite element model of normal shape. A boundary shape of a. disorder is assumed to be given as a reference displacement defined on a subboundary of the normal model based on medical images. We construct a problem to find the optimum deformation of the normal model that minimizes a square error integral on the subboundary between the hyper elastic deformation of the normal model and the boundary shape of the disorder by varying a design variable for density of the normal model. We show an evaluation method of the derivative of the square error integral of displacement with respect to the design variable, and a solution to the present problem by a gradient method. Finally, a numerical example for spine is introduced.