This paper proposes a design methodology for the robust observer using the eigenstructure assignment in multi-output systems so that the observer is less sensitive to the ill-conditioning factors such as unknown initial estimation error, modeling error and measurement bias in transient and steady-state observer performance. The robustness of the observer can be achieved by selecting the desired eigenvector matrix to have a small condition number that guarantees the small upper bound of the estimation error. So the left singular vectors of the unitary matrix spanned by space of the achievable eigenvectors are selected as a desired eigenvectors. Also, this paper proposes how to select the desired eigenvector based on the measure of observability and designs the observer with small gain. An example of a spindle drive system is simulated to validate the robustness to the ill-conditioning factors in the observer performance.