This paper proposes a new design method for a frequency‐dependent servo system for the positioning of flexible structures. In order to reduce sensor costs and to suppress spillover phenomena caused by ignored elastic modes of the plant, we introduce a prefilter into an input which possesses the characteristics of a notch filter. The proposed method allows for the design of the specified characteristics of the prefilter and for precise assignment of poles to desirable locations in a closed‐loop system. As a result, the tradeoff problem between suppression and transients can be resolved. The results of simulations and experiments are given in order to verify the usefulness of this method. © 2013 Wiley Periodicals, Inc. Electr Eng Jpn, 183(1): 39–50, 2013; Published online in Wiley Online Library (wileyonlinelibrary.com). DOI 10.1002/eej.22343