A method of defining three-dimensional structure from mask layout for computer simulation, which provides a technology for defining a three-dimensional structure of liquid crystal cell which comprises a apparatus of liquid crystal display for designing and analyzing a apparatus of liquid crystal display.A method of generating three-dimensional structure which comprised of material layers between upper substrate and lower substrate, which provides a generation method of three-dimensional structure for computer simulation by depositing material layers under the upper substrate and over the lower substrate, and sandwiching a center insertion layer between the deposited upper and lower material layers for a case which includes tapered structure of material layer for the substrate.