The mechanical properties of polycrystalline thin-films, critical for Micro-Electro-Mechanical Systems (MEMS) components, are known to have the size effect and the scatter in the length scale of microns by the numbers of intensive investigation by experiments and simulations. So, the consideration of the microstructure is essential to cover these length scale effects. The lattice based stochastic model for the microstructure evolution is used to simulate the actual microstructure, and the fast and reliable algorithm is described in this paper. The kinetics parameters, which are the key parameters for the microstructure evolution based on the nucleation and growth mechanism, are extracted from the given micrograph of a polycrystalline material by an inverse method. And the method is verified by the comparison of the quantitative measures, the number of grains and the grain size distribution, for the actual and simulated microstructures. Finite element mesh is then generated on this lattice based microstructure by the developed code. And the statistical finite element analysis is accomplished for selected microstructure.