The level set method has recently become popular in the simulation of semiconductor processes such as etching, deposition and photolithography, as it is a highly robust and accurate computational technique for tracking moving interfaces. In this research, full three-dimensional level set simulation has been developed for the investigation of focused ion beam processing. Especially, focused ion beam induced nanodot formation was investigated with the consideration of three-dimensional distribution of redeposition particles which were obtained by Monte-Carlo simulation. Experimental validations were carried out with the nanodots that were fabricated using focused Ga⁺ beams on Silicon substrate. Detailed description of level set simulation and characteristics of nanodot formation will be discussed in detail as well as surface propagation under focused ion beam bombardment.