This master thesis describes the development in the framework of Fluid- Structure Interaction (FSI) problems of an efficient and flexible technique treating the fluid-structure interface and mesh motion problems. The main idea is to build, through a new hierarchical approach, a tool with accurate identication capabilities for both the structural rigid movement (translation/rotation) and the elastic deformation (displacement), with the possibility of facing arbitrary structural and fluid discretization schemes. Starting from a review of the state of the art methods, used for these applications, the different shape representation techniques applied, like Free Form Deformation (FFD), Radial Basis Function (RBF) and Inverse Distance Weighting (IDW) are introduced and then compared to test their performances in terms of computational costs and achievable mesh quality. Then, in order to reduce the complexity of the geometrical model and its description, ad hoc innovative optimization techniques, like a selective approach of the RBF interpolation sites as well as a domain-decomposition approach for FFD, are presented showing clear reductions in term of computational costs. Some applications and test-cases, solved by using an open-source Finite Element library (LifeV), dealing with unsteady viscous (internal and external) flows, characterized by different Reynolds number, are shown to highlight the quality and the accuracy of the methods and their stability. For the implementation of the schemes developed, an efficient C++ object oriented code language was used, relying also on Trilinos packages.