A method for analyzing a structure includes processing nondestructive inspection (NDI) data for a multi-layer structure to define areas of inconsistency at an internal layer or an interface between adjacent layers. The method (500) includes mapping the areas of inconsistency to finite elements (404) of a finite element model (114) of a nominal of the structure. These finite elements are thereby identified as affected finite elements and include finite elements for the affected internal layer or interface. The method includes producing a reconstructed finite element model (116) of the affected structure (200) from the nominal finite element model, and a modified property or state value assigned to respective element datasets of the affected finite elements. The method includes performing a finite element method (FEM) failure analysis (110) of the reconstructed finite element model under a load, which indicates an extent of residual integrity of the affected structure.