This paper presents a comprehensive theoretical modeling for the laser assisted direct imprinting (LADI) process, which utilizes a quartz mold, pulsed laser heating, and contact pressure for direct nano-patterning and nanostructure fabrication on silicon substartes. The purpose of this work is to reveal the underlying mechanism behind LADI and to quantitatively characterize important imprinting parameters which dominate a successful LADI process. The theoretical modeling consists of three elements, the time-history of silicon melting when subjected to pulsed laser heating, the elastodynamic movement of mold's surface under resistance pressure, and the squeezing out of the molten silicon layer under the pressure from the walls. We have accurately determined the governing equations for each physical problems and derive the interaction relationship between them. A numerical scheme is developed to modeling the whole LADI process. The role of each important factor such as laser fiuence, contact pressure, viscosity of molten substance, and mold's feature size can be understood and visualized through this model and their influences on the final imprinting depth are also quantitatively determined.