Nowadays, facial mimicry studies have acquired a great importance in the clinical domain and 3D motion capture systems are becoming valid tools for analysing facial muscles movements, thanks to the remarkable developments achieved in the 1990s. However, the face analysis domain suffers from a lack of valid motion capture protocol, due to the complexity of the human face. Indeed, a framework for defining the optimal marker set layout does not exist yet and, up to date, researchers still use their traditional facial point sets with manually allocated markers. Therefore, the study proposes an automatic approach to compute a minimum optimized marker layout to be exploited in facial motion capture, able to simplify the marker allocation without decreasing the significance level. Specifically, the algorithm identifies the optimal facial marker layouts selecting the subsets of linear distances among markers that allow to automatically recognizing with the highest performances, through a k-nearest neighbours classification technique, the acted facial movements. The marker layouts are extracted from them. Various validation and testing phases have demonstrated the accuracy, robustness and usefulness of the custom approach.