A structural optimization engine generates a response profile based on a vibrational analysis of a three-dimensional (3D) structure. The structural optimization engine determines whether the 3D structure complies with one or more design goals set for the 3D structure based on the response profile. When the 3D structure does not comply with the design goals, the structural optimization engine retrieves dependency data from a structure database. The dependency data indicates various dependencies between response characteristics included in the response profile and specific regions of the 3D model. Based on the dependency data, the structural optimization engine determines structural modifications that can be made to the 3D structure to bring the 3D structure into compliance with the design goals. A multi-axis computer-aided manufacturing unit then makes the structural modifications to the 3D structure.