One embodiment of the present invention provides a system that efficiently conducts vibrational characterizations for a computer system having variable component configurations. During operation, the system receives a given component configuration associated with the computer system. Next, the system looks up the given component configuration in a resonant spectra library, which contains structural resonant frequencies for a number of possible component configurations for the computer system. If the given component configuration is found in the resonant spectra library, the system retrieves a set of structural resonant frequencies associated with the given component configuration. The system subsequently controls one or more vibration sources within the computer system to avoid the set of structural resonant frequencies.