Wear analysis performed on archaeological stone tools from prehistory aims at characterizing their surface alterations in order to determine their functions and describe past human technical behaviors. However, the reliability and repeatability of the method is questioned and there is a major difficulty facing scientists analyzing wear, which is related to proposing quantified and repeatable analyses and interpretations of taphonomic and anthropogenic (related to manufacture and use) evidence. We propose the creation of an experimental reference collection of surface alterations focused primarily on selected stone types commonly found at Hungarian archaeological sites. This collection will allow the characterization of the topographic signatures of manufacture, use, and taphonomic processes. The qualitative (through observation using optical microscopy) and quantitative (through surface measurements using confocal microscopy) analyses will aim at examining: 1) the variability of surface alterations, 2) protocols that can allow the identification and characterization of surface topographic signatures, and 3) the appropriate metrological setups that will allow for each of the alteration processes to be differentiated. We present here the results of the preliminary experiments, which involved flakes for bone and reed processing made of six different raw materials. It has been confirmed that evidence of use can be identified on each one of them. Beyond the presentation of the first images from the reference collection, we briefly present the future phases of the project.