Nowadays the nanostructures, formed on the way of self assembly are intensively investigated both in the basic and the applied sciences. In our paper, we investigate the structures on III-V compund semiconductor based materials, which are grown by epitaxial process. This process is analized by the beta version of Quantum Structure Analyzer 1.0, which is developed in C# langague, in the Microsoft© Visual Studio 2008 development environment. This software operates with the help of the Kohonen Self-Organizing Maps (SOM) algorithm and with the help of the Fuzzy C-Means algorithm. In present work, in the preface we give a short introduction of Molecular Beam Epitaxy (MBE), after this we introduce the algorithms, applied in this software. Finally, we demonstrate the results of the program. © 2013 IEEE.