Frequency response is characterized for mechanical components of a multirate system operating in a closed-loop environment. A disturbance is injected at the frequency of interest and at each of the alias frequencies thereof as an input into the multirate system, and a matrix equation composed of resulting measurements of the response of the multirate system is solved to compute the frequency response at the frequency of interest and at each of the alias frequencies. The resulting frequency response can be used to synthesize the transfer function of the entire system, which allows simulation and evaluation of the relative performance of multiple controller designs without the need for further frequency response measurements.