Raman microscopy has become a very useful tool to identify in situ micro-residues on prehistoric stone artefacts. The advantage of visually identifying material on a rock surface through a microscope objective, and then switching from white light to a laser beam focussed by the same objective to achieve sub-micron spatial resolution, makes it possible to obtain chemical and optical information from the same spot. Large numbers of spectra have to be collected to obtain representative data for each artefact, however, resulting in a large variety of possible residues. Not all of these residues are related to the original use of a stone tool. Here we report a key to assist in classifying residues identified by Raman spectroscopy with respect to their origin, including tool use and various sources of contamination (e.g., from the surrounding sediment or in the laboratory). We developed the key based on our experiences of using Raman spectroscopy as a primary investigative method to analyse stone tools from Liang Bua (Flores, Indonesia) and Denisova Cave (Altai Mountains, Russia), incorporating the stringent guidelines set by researchers using optical microscopy to identify residues related to tool use—namely micro-residue abundance and meaningful distribution in relation to visible traces of use-wear. We illustrate use of the key with archaeological and experimental tools.