Micro-machining is a widespread finishing process for fabricating accurate parts as biomedical devices. The continuous effort in reducing the gap between the micro- and macro-domains is connected to the transition from conventional to micro-scale machining. This process generates several undesired issues, which complicate the process’s optimization, and tool run-out is one of the most difficult phenomena to experimentally investigate. This work focuses on its analytical description; in particular, a new method to calibrate the model parameters based on cutting force signal elaboration is described. Today, run-out prevision requires time-consuming geometrical measurements, and the main aim of our innovative model is to make the analysis completely free from dimensional measurements. The procedure was tested on data extrapolated from the micro-machining of additively manufactured AlSi10Mg specimens. The strategy appears promising because it is built on a strong mathematical basis, and it may be developed in further studies.