A computer-implemented method is provided for use in finite element analysis of a three-dimensional (3D) representation of a physical object. The computer-implemented method includes combining a plurality of retained degrees of freedom of the 3D representation to form a root substructure, reducing a structure of the 3D representation on to a reduced automated multilevel substructuring (AMLS) subspace, and computing a plurality of eigenmodes and condensed operators based on the reduced structure, and computing constraint modes using an AMLS transformation matrix. The computer-implemented method also includes generating at least one substructure of the 3D representation based on the plurality of eigenmodes, constraint modes, and condensed operators, and storing the at least one substructure in a memory area.