This paper discusses a method of filling in a gap in consistency between a real world situation and an application within Model Driven Architecture (MDA). In the MDA this consistency is foreseen but not developed. The suggested method uses formalization capabilities of a topological functioning modeling and universal categorical logic. The main idea is that a problem domain is represented by a topological space from a computation independent viewpoint, whereof a topological functioning model of the system under consideration is separated by the closure operation. Further, this model is constrained by functional requirements for the application and conformed to system users’ goals expressed in UML constructs. The main advantage of the suggested method is making consistent functionality of the problem domain and the solution at the very beginning of analysis.