This paper describes the place and usage of a topological model of system functioning in the framework of OMG’s Model Driven Architecture. In this paper we suggest the formal method of constructing a topological model of system functioning. The topological functioning model shows a system from the computation independent viewpoint as a mathematical topological space of functional features interconnected by cause-and-effect relations. Topological and functional properties of the model allow formal identification of a system model from the topological space of an environment, model refinement and abstraction. The topological functioning model allows capturing information in a formal way at the very beginning of software development, thus it gives a well-defined opportunity to get a high-quality end result within the framework of MDA. The suggested method supposes formal obtaining of the system model from the informal verbal description of the system. The main stages of the method, which are described in this paper, are as follows: system inner object identification, external system identification, system functional feature definition, cause-and-effect relation identification among the found functional features, and topological model of system functioning mathematical separation from the topological space of system environment. The described method is explained in detail and illustrated by an example of library functioning.