The present disclosure provides for a system and method for analyzing questioned documents. A sample document is illuminated to thereby generate a first plurality of interacted photons. The first plurality of interacted photons are detected at a first detector to thereby generate a digital image. The digital image is analyzed to thereby identify at least one region of interest of the sample document. This region of interest is illuminated to thereby generate a second plurality of interacted photons. This second plurality of interacted photons are passed through a tunable filter and detected at a second detector to thereby generate a hyperspectral image representative of the region of interest. The hyperpsectral image may then be analyzed to evaluate changes to or differentiate different inks present in the sample document. Chemometric techniques such as k-means clustering, PCA, and/or PLSDA may also be applied.