Close-packed monolayer silica spheres organized through a self-assembly process have been widely used in micro/nano fabrications. In this study, we present the effects of substrate on the near-field enhancement of microsphere-assisted laser processing. There are significant differences in the surface morphology of sub-micro hole arrays on substrates with different refractive indices, which were fabricated at the same laser fluence by a KrF excimer laser (lambda=248 nm). It is found that the position of the maximum enhancement removes from the exit surface of the silica sphere into the sphere as the refractive index of substrate increased based on the simulation. In addition, the field distribution curve oscillates when there is a substrate under the microsphere, and oscillation spreads deeper into the substrate with a high refractive index. The results contribute toward the optimization of the process conditions of the microsphere-assisted laser micro/nano patterning technique and make the modification profile of the material more controllable. (C) 2015 Elsevier B.V. All rights reserved.