A special MatViz3D application was developed for computer modeling of the process of crystallization and generation of microstructures. The main advantages of the application are: three-dimensional generation of microstructures, which allows researchers to obtain detailed and realistic images of the structure of the material, the selection of the neighborhood of cells for the variety of generation, and the possibility of following the step-by-step process of crystallization. Overall, MatViz3D is a powerful tool for modeling, analyzing and visualizing the microstructures of materials using a variety of approaches and techniques.