In this study, a hybrid approach coupling hyperspectral near infrared imaging with a progressive finite element method is proposed for characterization of the elastic and failure response of composites with non-uniform variations of the wrinkles profile through the thickness and across the structure dimensions. In this approach, hyperspectral near infrared spectroscopy is used to create a 3D profile of the surface resin pockets with the capability of measuring resin thickness from approximately 125 to 2500 μm. These resin pockets are directly correlated to underlying ply level wrinkling as confirmed by optical microscopy. The 3D mapped resin plane obtained from the hyperspectral imaging is used to morph a ply-by-ply finite element model of a carbon-fiber/epoxy resin laminated plate using a progressive damage failure methodology. The results show the capability of the hybrid method to predict the structural response in laminated composites containing spatially distributed and non-uniform ply-level wrinkling.