In order to realize high productivity and reliability of the modern semiconductor fabrication, defects inspection techniques for the layers of SOI (Silicon On Insulator) wafer become more essential. The layers on SOI wafer have only about 100~200nm thickness, at present, the technique of evaluating appropriately the defects in such thin layers does not exist. Novel optical defect measurement method to detect and classify the nano-defects that exist in the layers of SOI wafers by using evanescent field is proposed. In this method, propagating infrared laser in the layer generates evanescent field, which is affected by the defects existing on and below the surface. To execute light coupling into the layer, the prism coupler that is made of single crystal silicon was developed. In this paper, first the electromagnetic field in near-field of the wafer surface vicinity was analyzed by using FDTD (Finite Difference Time Domain) simulation tool. The results show this method can detect and classify the nano-meter scale defects on the surface and in the layers. Next the fundamental experiment was carried out to detect defects like sub-micrometer diameter hole that was fabricated on SOI wafer using FIB (Focused Ion Beam) machining. The experimental result also shows this method can detect the defects on the surface of SOI wafers sensitively.