In this paper, an efficient numerical procedure is proposed, adapted to the modal analysis of a fully-loaded spent nuclear fuel canister, which exhibits distinct structural levels associated with a hierarchy of components. On the one hand, the fully-loaded spent nuclear fuel canister is constituted of the repetition of identical components, resulting in a pseudo-periodicity; and the components of a given level are separated from each other and only connected to their upper level through localized attachments, which gives rise to an advantageous structural connectivity that can be exploited for efficiency. On the other hand, the necessary fine mesh resolution of the small levels leads to a high-dimensional computational model and, in addition, the independent resonant vibrations of each of the components produce a very large number of vibration eigenmodes. The aforementioned opportunities and difficulties are respectively leveraged and tackled by an adapted method that combines domain decomposition, shift-invert Lanczos eigenvalue solver, and Craig-Bampton substructuring technique. A parallel eigensolution via spectrum slicing is facilitated by an efficient block factorization by Schur complement that is enabled by the sparsity of the Craig-Bampton matrices. A computational gain of four orders of magnitude is obtained, at the expense of negligible errors that are exactly characterized. The proposed methodology enables a high-fidelity vibration analysis of the sealed fully-loaded spent nuclear fuel canister, useful for non-intrusive inverse identification of the structural integrity of the internal structural levels holding the nuclear material.