The growth of GaN on the patterned substances has proven favorable to achieve thick, crack-free GaN layers. Based on these methods, we specially designed periodically patterned Si substrate process, which is referred to as lateral epitaxy on patterned Si substrate (LEPS). High crystalline quality GaN are obtained by using this technique. In this paper, numerical modeling of transport and reaction of species is performed to estimate the growth rate of GaN from the reaction of trimethyl gallium (TMG) and ammonia. The effect of fabricated structure of feature scale model will be predicted by using the topography simulator, and deposition profile of the GaN on the pattern will be discussed. The effect of flow conditions and pattern shape and periodicity will also be addressed, which can be critical for the quality of crystal growth. The dependency of step coverage and conformality of patterned mask will also be discussed. (C) 2007 Elsevier B.V. All rights reserved.