As part of an effort to improve emissions, noise, and performance of next generation aircraft, it is expected that future aircraft will use distributed, multi-objective control effectors in a closed-loop flight control system. Correlation challenges associated with parameter estimation will arise with this expected aircraft configuration. The research presented in this paper focuses on addressing the correlation problem with an appropriate input design technique in order to determine individual control surface effectiveness. This technique was validated through flight-testing an 8.5-percent-scale hybrid-wing-body aircraft demonstrator at the NASA Dryden Flight Research Center (Edwards, California). An input design technique that uses mutually orthogonal square wave inputs for de-correlation of control surfaces is proposed. Flight-test results are compared with prior flight-test results for a different maneuver style.