A manufacturing control system for an additive, subtractive, or hybrid machining system implements a morphic manufacturing approach that integrates in situ inspection and related decision-making into the manufacturing process. After execution of a machining or deposition operation, the system performs a sensor scan to collect sensor measurement data for the resulting part while the part remains in the manufacturing work cell. The measurement data is compared with an as-designed digital model of the part to determine whether further machining or deposition is necessary to bring the finished part into tolerance with the model. If necessary, the system performs another additive and/or subtractive manufacturing operation on the part based on analysis of the measurement data to bring the part into tolerance. The measured inspection data can be stored in association with each manufactured part for auditing purposes or for creation of part-specific digital twins.