Methods and systems for obtaining numerically simulated structural behaviors of layered composite materials within a structure in a time-marching simulation using finite element analysis (FEA) are disclosed. A single identifier is used for designating all shell finite elements representing parts or components made of layered composite materials in a FEA model of a structure by user. Layered composite materials may have arbitrary number of layers. Each layer may have different material orientation/angle or fiber direction, thickness, and structural material behaviors. Each shell element representing composite material includes a set of through-thickness integration points with each corresponding to one layer of the layered composite materials. The shell elements are sorted by types into a number of internal groups to facilitate vectorization and/or more optimal domain decomposition in massive parallel processing. The internal groups are configured to be hidden from the user and stored in contiguous memory locations when conducting a FEA.