Reconfigurable multivariable flight control using an indirect adaptive algorithm is proposed for aeroservoelastic (ASE) instability and flutter suppression in the presence of aircraft system failure or battle damage. A reduced order procedure using an effective and rigorous proper orthogonal decomposition technique (POD) is adopted to reduce all critical modes collected from an offline instability study called massive failure screening. It acquires the flutter/ASE sensitivity parameters using a unique computational aeroelastic/aeroservoelastic MDO/Analysis software tool ASTROS*/ASE, developed and advanced by ZONA under AFRL support since 1996. Massive failure screening and POD are essential techniques that will promote the efficiency of the parameter estimation for real-time system identification. Selection of optimal sensor locations and the on-line search and comparison of the critical modes with sensor outputs can then follow. The minimum variance control scheme proposed is a very efficient optimal scheme for output response minimization. Continuous on-line monitoring will be applied to the control system except the minimum variance control. Switch-on gauge is based on a threshold whenever impact or diverged responses overrides the gust/white noise levels. F/A-18 will be used as the baseline aircraft to demonstrate and validate the proposed reconfigurable controller in terms of its algorithm stability, efficiency, effectiveness to flutter/ASE instability, fault-tolerance, and overall performance with cost considerations.