Substrate scratches can limit the laser resistance of multilayer mirror coatings on high-peak-power laser systems. To date, the mechanism by which substrate surface defects affect the performance of coating layers under high power laser irradiation is not well defined. In this study, we combine experimental approaches with theoretical simulations to delineate the correlation between laser damage resistance of coating layers and the physical properties of the substrate surface defects including scratches. A focused ion beam technique is used to reveal the morphological evolution of coating layers on surface scratches. Preliminary results show that coating layers initially follow the trench morphology on the substrate surface, and as the thickness increases, gradually overcoat voids and planarize the surface. Simulations of the electrical-field distribution of the defective layers using the finite-difference timedomain (FDTD) method show that field intensification exists mostly near the top surface region of the coating near convex focusing structures. The light intensification could be responsible for the reduced damage threshold. Damage testing under 1064 nm, 3 ns laser irradiation over coating layers on substrates with designed scratches show that damage probability and threshold of the multilayer depend on substrate scratch density and width. Our preliminary results show that damage occurs on the region of the coating where substrate scratches reside and etching of the substrate before coating does not seem to improve the laser damage resistance.