Searching for new ways to improve the efficiency of integrated circuits (IC) led to the development of specialized heterogeneous configurable IC (FPGA) and systems-on-a-chip. Their key feature is an extended interpretation of standard cell library, containing ready-to-use IP cores along with standard cells. Specific customer designs require the flexibility of the configurable heterogeneous IC’s architecture and, therefore, automatic CAD clustering and placement algorithms configuration. The development of efficient configuration methods and algorithms is impossible without relying on the mathematical apparatus. In this work, such mathematical apparatus is provided. The authors described a set-theoretic model of a hierarchical project and formalized the hierarchical approach to the netlist, using the apparatus of mathematical logic, set and graph theories. The correspondence between the customers designs’ elements and FPGA’s elements has been formalized to provide fast clustering and placement configuration. The obtained results provide the basis for future efficient methods for automatic placement and clustering configuration.