In a moving base simulator, the eigenmodes of the simulated vehicle are perceived as distorted due to the added dynamics of the motion filter. The Eigenmode Distortion (EMD) method evaluates flight simulator motion cueing fidelity based on the perceived distortion of relevant eigenvectors of specific vehicle dynamics. This method was previously applied to models of the AH-64 Apache and the Cessna Citation II. The goal of this study is to investigate the use of EMD in structured tuning of a motion cueing algorithm (the classical washout algorithm (CWA)) for CH-47 simulation, and to identify whether the resulting filter is rated better, according to the motion fidelity rating (MFR), than manually tuned filters. To this end, the EMD filter is compared, in an experiment, to a manually tuned filter, which is currently in use at Desdemona for CH-47 simulations. The CH-47 EMD filter is also compared to an EMD motion filter, tuned for the AH-64 Apache in a previous experiment, in order to test whether a single EMD filter can or cannot be used for different vehicles. In this experiment, three pilots participated, with experience in flying the CH-47 helicopter. The results of this experiment show a preference for the vehicle-specific, EMD-based approach, based on which it can be said that EMD is preferred, by the participating pilots, over current, manual tuning methods.