Transformation from model to model significantly facilitates the construction of software system structures. This paper offers the software system structure construction by means of topology which is borrowed from Topological Functioning Model (TFM). TFM uses mathematical foundations that holistically represent complete functionality of the problem and application domains and therefore can be used for software system structure construction. Application of TFM within software development process enables formal analysis of business system and formal designing of system structure. Software development begins with TFM creation. After construction of business system’s TFM by applying transformation on TFM a system structure is defined. As a basis for system structure definition is used problem domain object graph and sequence diagram. Sequence diagram is constructed with problem domain object graph and TFM.