In this paper, an experimental verification of system identification technique for constructing finite element model is conducted for a three-story test structure equipped with an active mass driver (AMD). Twenty Gaussian white noises were used as the input for AMD, and the corresponding accelerations of each floor are measured. Then, the complex frequency response function (FRF) for the input, the force induced by the AMD, was obtained and subsequently, the Markov parameters and system matrices were estimated. The magnitudes as well as phase of experimentally obtained FRFs match well with those of analytically obtained FRFs.