The control of flexible systems is often difficult due to the exact frequencies of the elastic modes being hard to identify. These flexible modes may change over time, or vary between units of the same system. The variation in the modal dynamics may cause a degradation in performance or even instabilities unless compensated for by the control scheme. Controllers designed for these types of systems use notch filters for mode suppression. However variation in the parameters of the flexible modes may cause the need for wide notch filters. An adaptive scheme is proposed which uses an online estimator based on plant parameterization. The scheme may not use probe signals and may not rely on exact parameter identification of the unknown parameters. Instead it may continuously update itself to cancel the effect of the flexible modes by been able to identify the effect of the modal dynamics on the performance of the system. The adaptive notch filter can be designed narrower, adding less phase lag at lower frequencies, thereby allowing an increase in bandwidth and disturbance rejection capability. Simulation and experimental verification of the adaptive mode suppression scheme is given through the use of a laser beam pointing system. The adaptive scheme is compared to a non-adaptive scheme, and is able to decrease the standard deviation of the experimentally measured tracking error by 14% even when the flexible dynamics are unknown.