A newly developed semi-fixed flexible polishing tool called sol-gel (SG) polishing pads can satisfy the polishing demand of silicon wafers with scratch-free and nanoroughness surface. However, an obvious damage layer emerges on the surface of monocrystalline silicon wafer after polished by SG polishing pads with diamond abrasives. In this paper, combined characterizations consist of grazing incidence X-ray diffraction, Raman spectroscopy (RS), focused ion beamscanning electron microscopy (FIB-SEM), transmission electron microscopy (TEM), and SEM were used to observe the damage layer together with the polishing residue. The results indicated that the surface monocrystalline silicon transformed to α-Si and nano-Si. Analysis on the polishing processes under the same experimental parameters with different tools and abrasives revealed that the material removing scale about 100-300 nm may account for the generation of damage layer.Index Terms-Sol-gel (SG) polishing pads, silicon wafer, diamond abrasives, damage layer.