Orthogonal eigenstructure control is a novel control method that can be used for vibration suppression in flexible structures. The method described in this study does not need defining the desired locations of the closed-loop poles or predetermining the closed-loop eigenvectors. The method, which is applicable to linear multi-input multi-output systems, determines an output feedback control gain matrix such that some of the closed-loop eigenvectors are orthogonal to the open-loop eigenvectors. Using this, the open-loop system’s eigenvectors as well as a group of orthogonal vectors are regenerated based on a matrix that spans the null space of the closed-loop eigenvectors. The gain matrix can be generated automatically; therefore, the method is neither a trial and error process nor an optimization of an index function. A finite element model of a plate is used to study the applicability of the method to systems with relatively large degrees of freedom. The example is also used to discuss the effect of operating eigenvalues on the process of orthogonal eigenstructure control. The importance of the operating eigenvalues and the criteria for selecting them for finding the closed-loop system are also investigated. It is shown that choosing the operating eigenvalues from the open-loop eigenvalues that are farthest from the origin results in convergence of the gain matrix for the admissible closed-loop systems. It is shown that the converged control gain matrix has diagonal elements that are two orders of magnitude larger than the off-diagonal elements, which implies a nearly decoupled control.