The surface profile is an important specification that influences the performance and stability of a microelectromechanical system device. Microscopic interferometry is, up to now, the most widely used technique for surface profiles of microstructures. A long working distance is needed when it is necessary to place components such as probes or transparency windows between microstructures and the objective. In this paper, a long-working-distance Linnik microscopic interferometer system was developed for meeting above requirements. Because it is difficult to ensure that the sample and the reference objectives are completely identical, the surface profile is modulated by unmatched optical path length between measurement and reference arms. This paper puts forward compensation process for demodulating the surface profile. Experiment results show that this method can provide correct measurement of the surface profile of microstructures effectively.