One embodiment of the present disclosure provides a system for determining a hybrid-manufacturing plan for manufacturing an integrated circuit (IC). During operation, the system can obtain a set of hybrid-manufacturing constraints for manufacturing the IC. The set of hybrid-manufacturing constraints can include a set of primitives, a set of atoms, and an atom end-state vector. An atom can correspond to a unit of spatial volume of the IC. A primitive can represent an additive, subtractive, or a mixed manufacturing process corresponding to one or more atoms of the IC. Next, the system can determine a plurality of feasible hybrid-manufacturing plans based on the set of manufacturing constraints. Each feasible hybrid-manufacturing plan can represent an ordering of the set of primitives that satisfies the atom end-state vector. The system can then determine costs for manufacturing the IC using the plurality feasible hybrid-manufacturing plans. The system can determine, based on the costs, an optimized hybrid-manufacturing plan for manufacturing the IC.