Nondestructive characterization on thin films and their stack in MOEMS device is highly desirable. But, it is often a challenging task because the area is usually small. During processing of thin films, the deposition rates, optical properties, and mechanical properties must be fully understood to fabricate a device with desired performance. With the patterned surface, deposition rate of a typical physical vapor deposition (PVD) technique, such as electron-beam evaporation and sputtering, varies at different location due to shadow effect. In this study, spectroscopic ellipsometry and reflectometry were used to characterize the optical properties of electron-evaporation thin films on a flat substrate. On the other hand, microreflectometer was used to monitor the spectrum of deposited multi-stack of optical thin films inside via-holes. Combination of these two techniques provides a practical way to qualify the processing and ensure the device performance.