In order to carry out the alignment of non-rigid models a general transformation is required, which includes a rigid transformation and a deformation. In this work, we present a system that uses Radial Basis Functions to obtain the non-rigid transformation. Although modeling deformable objects using these functions is not a physical modeling, it is computationally faster compared with the methods based on physics like the mass-spring systems and the finite element analysis. This last one is used like a reference, since it allows approximating the deformation with high accuracy. A comparison is done between the deformation obtained with the different radial basis functions used: Gaussian, multiquadrics and inverse multiquadrics, and that one obtained through finite element analysis. The system is evaluated on four synthetic models.