In an Industry 4.0 context, to each object a "digital twin" is associated, which is a virtual counterpart of the object itself. In the case of a tool this includes, together with its material and manufacturing information, its solid geometry. Tool geometry knowledge is fundamental to enable effective tool management, manufacturing verification, and tooling simulation. If for tool management, the conventional 2D presetting is sufficient, tooling simulation and tool manufacturing verification require a complete 3D characterization. This is particularly true in the case of the microtools: the process of micro-chip formation is still a research subject.Although the 3D geometry of tool is well established in the ISO 3002 series of standard, only recently 3D measurement of tools has been made possible by new measuring systems. Still, tool geometry verification requires a lot of human intervention.This paper aims at setting the base for the automatic analysis point mesh scanned on the whole surface of tools, and in particular microtools.The first step for doing this is the identification of the active surfaces of the tool, that is the face and the flank plus the cutting edge. The identification of these geometric features is in general possible thanks to their specific characteristics: in particular, the cutting edge is characterized by a high curvature, and it separates the face from the flank. This paper considers cylindrical micro end-mills as a first example of an approach that can be extended to in principle any kind of tool. The cylindrical helix characterizing the cutting edge is the key geometry to be considered in the development of the specific method. Once the tool features (face, flank, and cutting edge) have been separated, of the tool angles, for instance, can be estimated. As first angle to study, the rake angle has been selected. The approach will be validated on simulated data and on real scans of micro-tools.