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