In modern IC fabrication technology, metal silicide technology in microelectronics has been a standard process to reduce contact resistance. The thickness of metal silicide is an important parameter in reducing the contact resistance, especially, the 130nm, 90nm, and beyond technology. The traditional method to measure the thickness of silicide, however, has a dilemma as to whether to obtain the clear interface or to get the true thickness. This paper reports a novel method to improve the interface contrast and get a true thickness by changing the substrate single crystal contrast. Polishing and ion milling method were used to get thin transmission electron microscopy samples. In this paper, the substrate scattering probability is changed by tilting the samples. Using the method, a clear interface can be developed between the silicide and substrate single crystal silicon can be obtained without affecting the accuracy of the measured silicide thickness.