We examine sub-structuring methods for solving large-scale generalized eigenvalue problems from a purely algebraic point of view. We use the term "algebraic sub-structuring" to refer to the process of applying matrix reordering and partitioning algorithms to divide a large sparse matrix into smaller submatrices from which a subset of spectral components are extracted and combined to provide approximate solutions to the original problem. We are interested in the question of which spectral componentsone should extract from each sub-structure in order to produce an approximate solution to the original problem with a desired level of accuracy. Error estimate for the approximation to the small esteigen pair is developed. The estimate leads to a simple heuristic for choosing spectral components (modes) from each sub-structure. The effectiveness of such a heuristic is demonstrated with numerical examples. We show that algebraic sub-structuring can be effectively used to solve a generalized eigenvalue problem arising from the simulation of an accelerator structure. One interesting characteristic of this application is that the stiffness matrix produced by a hierarchical vector finite elements scheme contains a null space of large dimension. We present an efficient scheme to deflate this null space in the algebraic sub-structuring process.