The two kinds of 3ω harmonic separator were prepared by electron beam evaporation with different materials. Laser induced damage threshold (LIDT) was measured at 1064 nm and the damage morphologies were mapped by Alpha-Step 500 meter. It was found that there are two different damage geometries: shallow denudation and deep crater. Shallow denudation in a certain range had same depth at different energy fluences, and material was removed from the top film layers. Deep crater had different depths caused by the combination of melting vaporization and fracture of inner defects of coatings, which was the main cause for decreased damage threshold.