A structure health monitoring ("SHM") system according to the invention can be deployed in an onboard environment, such as an aircraft, to provide an ongoing damage assessment of structural components on the aircraft. The SHM system reduces or eliminates time consuming and costly manual inspections of aircraft. The SHM system can leverage known sensor technologies to collect sensor data indicative of the structural health of the monitored components. The sensor data is processed and baselined with sensor feature baselines and damage estimate baselines to provide an accurate final damage estimate for the monitored component. The final damage estimate can be further processed or formatted for compatibility with aircraft maintenance systems.