Substructuring and superelements technique is today one of the most important procedures in large scale stress analysis industry design processes. In this thesis the implementation of substructuring and superelements technique in finite element method is presented, with its application in various types of one, two and three – dimensional problems in stress analysis of thin-walled structures. As a ground basis needed to develop substructuring procedure with FEM, first the programming procedures of the classical FEM in Matlab programming language are presented in the Appendix, alongside with the application of classical FEM in two – dimensional plane stress analysis problems. For the plane stress analysis problems solved in Appendix the programming codes were developed using repository of professor dr. sc. Jack Chessa (University of Texas) called FEMLAB [1], as a basis. Analysis performed in Appendix is serving as an essential foreknowledge needed for the substructuring and superelements approach to be implemented and applied. As for the main part of the thesis, first an overview of FEM implementation in structural analysis is presented. Substructuring and superelements technique is introduced. Physical and mathematical concept of the technique is developed, with the practical aspects emphasized and singled out. Global – local analysis (two levels) is distinguished from multilevel substructuring. The procedure of substructuring is described in detail, with the given data flow diagram in generic multilevel substructuring made of any desired number of levels. Programming concept of the technique is thoroughly described, and the interface between an external mesh generator (Gmsh) and Matlab programming language is developed. The procedure of substructuring was performed with the “top – down” approach, whilst the programming procedure was implemented in both directions, “top – down” and “bottom – up”. The substructuring procedure and its programming are then connected together in application to a set of one, two and three – dimensional problems in stress analysis of thin – walled structures. One – dimensional bar element is solved using this technique by hand, to illustrate the need of programming the procedure for more complex problems. The two – dimensional problems were solved using an automated approach programmed in Matlab, and a thin plate with a non-symmetrical hole subjected to an in-plane bending load is analysed by diving it into a total of ten level two substructures. Programming the technique in 3D is then illustrated through an example of a simple hexahedron case made up of 6 thin plates. Eventually, built on the knowledge collected through working on this thesis, a stress analysis of a 3D ship cover with one bulkhead is performed, according to the drawing made in Catia. Practical aspects of the technique are directly pointed out and emphasized through the analysis of processing and its results, whose visualization, alongside with Matlab, is presented in Paraview Visualization Toolkit. The thesis finishes by describing a concept idea of how to manipulate with large data structures, such as the one obtained and collected through performed analysis of a 3D ship cover.