The pursuit of innovative ship designs, the use of new materials, and the increasingly demanding performance requirements dictate a broadly focused thrust for addressing noise and vibration issues during the design process. This expanded technical view also requires that the types of tools used for these assessments can provide results within a short enough time to affect the design cycle. Recently, an Energy Finite Element Analysis (EFEA) formulation has been developed for computing the vibration and the associated radiated noise of complex vehicles at frequencies where conventional finite element methods are no longer efficient. In this paper the main theoretical aspects of the EFEA are presented first. Next, a substructuring capability is described where large computational models, typical of naval applications, can be subdivided into separate domains for pursuing a compartmentalized solution and achieving further improvements in computational efficiency. Finally, validation case studies are presented with correlation between computations and scaled model testing.