Experts' opinions exist that the way software is built is primitive. The role of modeling as a treatment for Software Engineering (SE) became more important after the appearance of Model-Driven Architecture (MDA). The main advantage of MDA is architectural separation of concerns that showed the necessity of modeling and opened the way for Software Development (SD) to become engineering. However, this principle does not demonstrate its whole potential power in practice, because of a lack of mathematical accuracy in the initial steps of SD. The question about the sufficiency of modeling in SD is still open. The authors believe that SD, 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 an important part of SE in its real sense. They introduce such mathematical formalism by means of topological modeling of system functioning.