PFFEM software, PFADS has been developed for the vibration predictions and analysis of coupled system structures in medium-to-high frequency ranges. PFFEM is numerical method which solves energy governing equation using finite element technique for complicated structures where the exact solutions are not available. Through the upgrades, present PFADS R3 could cover the general beam and plate structures including various kinds of beam-plate rigid joints and other joint systems such as spring-damper junction and rigid bar connection. This software is composed of 3 parts; translator, model converter and solver. The translator makes its own FE-model from bulk data of commercial FE software, and the model converter is used to convert FE-model to PFFE-model automatically. The solver calculates vibrational energy density and intensity for PFFE-model by solving global matrix equations of PFFEM. For the applications of real transportation systems, a container ship model has been examined with respect to major parameters, and reliable results have been obtained.