The authors share with some other experts the opinion that the way software is built is primitive. Therefore, this chapter discusses a role of modeling as a treatment for software engineering. The role of modeling became more important after appearance of principles proposed by Model Driven Architecture (MDA). The main advantage of MDA is architectural separation of concerns that showed necessity of modeling and opened the way to software development to become engineering. However, the weakness is that this principle does not demonstrate its whole potential power in practice, because of a lack of mathematical formalism (or accuracy) in the very initial steps of software development. Therefore, the question about the sufficiency of modeling in software development is still open. The authors believe that software development in general, and modeling in particular, based on mathematical formalism in all its stages together with the implemented principle of architectural separation of concerns can become Software Engineering in its real sense. The authors introduce such mathematical formalism by means of topological modeling of system functioning.