The inverse Finite Element Method (iFEM) is receiving more attention for shape sensing due to its independence from the material properties and the external load. However, a proper definition of the model geometry with its boundary conditions is required, together with the acquisition of the structure’s strain field with optimized sensor networks. The iFEM model definition is not trivial in the case of complex structures, in particular, if sensors are not applied on the whole structure allowing just a partial definition of the input strain field. To overcome this issue, this research proposes a simplified iFEM model in which the geometrical complexity is reduced and boundary conditions are tuned with the superimposition of the effects to behave as the real structure. The procedure is assessed for a complex aeronautical structure, where the reference displacement field is first computed in a numerical framework with input strains coming from a direct finite element analysis, confirming the effectiveness of the iFEM based on a simplified geometry. Finally, the model is fed with experimentally acquired strain measurements and the performance of the method is assessed in presence of a high level of uncertainty.