This paper introduces a new algorithm that allows for the efficient generation of large substructures using automated multi-level substructuring (AMLS) technology. Generally, the conventional substructure generation algorithms require two computational steps to generate a substructure; the first step is a substructure mode generation step to compute constraint modes and dynamic modes, and the second step is a condensed model generation step to compute condensed operators (including stiffness, mass, viscous and structural damping matrices, and force vectors) using the substructure modes computed in the first step. In this conventional algorithm, full-scale constraint modes and dynamic modes are essential to compute the final condensed operators. The new algorithm combines these two steps into one process, so that all the condensed operators are generated during the AMLS eigensolution procedure without a mandatory requirement of full-scale constraint modes and dynamic modes.This new algorithm was implemented within the AMS eigensolver, so that the performance benefits of the new algorithm can be presented by comparing its performance with the performance of the conventional approach. It is demonstrated that computational times and the disk space requirement of the new substructure generation procedure are significantly reduced compared to the conventional two-step implementation.