The surface structure features of conventional polished and magneto-rheological finishing (MRF) polished fused silica are characterized by HF based etching and thermal treating combined with atomic force microscopy (AFM). To analyze the source of thermal treating bulges, the polished surfaces are treated by three different surface treatments, namely, ultrasonic cleaning, chemical leaching, and HF etching to remove different materials on/in surface. The surface morphology after etching or thermal treating and their correlations show that there existe high-density nanoscale defects in conventional polished surface. These subsurface defects are composed of nanoscale micro-cracks and grainy impurities, which are easy to induce laser damage. Herein, a micro-cracks and grainy impurities structure model about conventional polished surface is proposed based on the analysis of material removal mechanism of polishing.