Monitoring mechanical systems operating in uncertain environments contaminated with both environmental disturbances and noise lead directly to low signal-to-noise-ratios, creating an extremely challenging processing problem, especially in real-time. In order to estimate the performance of a particular system from uncertain vibrational data, it is necessary to identify its unique resonant (modal) frequency signature. The monitoring of structural modes to determine the condition of a device under investigation is essential, especially if it is a critical entity of an operational system. The development of a model-based scheme capable of the on-line tracking of the inherent structural modal frequencies by applying both constrained subspace identification techniques to extract the modal frequencies and state estimation methods to track the evolution is discussed. An application of this approach to a cylindrical structural device (pipe-in-air) is analyzed based on theoretical simulations along with controlled validation experiments, including injected anomalies illustrate the approach and performance. Statistics are gathered to bound potential processors for real-time performance employing these constrained techniques.