A fluorescence fingerprint (FF), also known as an excitation-emission matrix, is a set of fluorescence spectra acquired at consecutive excitation wavelengths, producing a three-dimensional diagram. The pattern of this diagram is unique for every constituent, similar to a fingerprint. The FF technique has an advantage over conventional fluorescence spectroscopy because it includes emission spectra excited at many different excitation wavelengths, making it possible to measure complex samples that contain many fluorophores. In this paper, applications of FF technology for discriminating the geographic origin of mangos and aerobic plate count prediction on the surface of sliced beef are presented. We also introduce the combination of FF and imaging techniques for visualizing the internal structure of soybean samples. Finally, an algorithm for designing optimal FF filters and its feasibility for simplifying, reducing the cost, and increasing the speed of FF measurements are discussed.