Simulations of SON structures were carried out by the use of FEM and the arbitrary Lagrangian-Eularian (ALE) method through the software COMSOL Multiphysics®. A novel time-dependent“virtual” curvature algorithm based on non-linear surface diffusion kinetics for FEM simulations is presented. The model describes the evolution from a cylindrical trench etched on silicon to an equilibrium sphere by thermal annealing. An initial aspect ratio (length/diameter) of 2.22-6.66 is determined for creating an ESS. For more than one ESS, the aspect ratio limits are also investigated. With this model, at equilibrium, the step size increases with the length of the initial trench once it is closed while the SON layer increases with the initial cylindrical depth. The temperature enhances the velocity of the evolution.