For the conventionally polished fused silica substrate, an around 100 nm depth redeposition polishing layer was formed on the top of surface. Polishing compounds, densely embedded in the redeposition polishing layer were the dominant factor that limited the laser induced damage threshold (LIDT) of transmission elements in nanosecond laser systems. Chemical etching, super-precise polishing and ion beam etching were employed in different ways to eliminate these absorbers from the substrate. After that, Antireflection (AR) coatings were deposited on these substrates in the same batch and then tested by 1064 nm nano-pulse laser. It was found that among these techniques only the ion beam etching method, which can effectively remove the polishing compound and did not induce extra absorbers during the disposal process, can successfully improve the LIDT of AR coatings.