We present a benchmarking framework to design multi spectral systems working in the NIR range for multiple purposes. This framework is composed of a hyperspectral imaging hardware and an ad-hoc software that performs pattern recognition experiments (image acquisition, segmentation, feature extraction, feature selection, classification and evaluation steps) comparing different algorithms in every step. For each experiment, we obtain a solution using a generic hyper spectral system, but we also obtain enough data to design a specific multi-spectral system in order to decrease the overall execution time. This improvement is based in the feature se lection step, that provides the most relevant wavelengths for the problem. The framework has been tested for detecting internal and external features in potatoes, determining the origin of honey, and studying fecundity parameters in hen eggs.