In this paper an interactive computational methodology was developed assuming that shape and size optimization of flexible components can significantly improve energy absorption or storage ability in assembled systems with flexible components (AS-FC). A radial basis functions mesh morphing formulation in non-linear numerical finite element analysis, including contact problems and flow interaction, was adopted as optimal design method to optimize shape and size design parameters in AS-FC. Flexible components were assembled in finite element environment according to functional ISO-ASME tolerances specification; non-linear structural analysis with flow interaction analysis was performed. The results of the study showed that the proposed method allows to optimize the shape and size of the flexible components in AS-FC maximizing the system's ability to absorb or store energy. The potentiality of the method and its forecasting capability were discussed for the case study of an automotive crash shock in which the specific energy absorption was increased by over 40%. The case studied refers to a simple flexible component geometry, but the method could be extended to systems with more complex geometries.