This article proposes a new method to perform the referencing procedure between the workpiece and small portable machines that can move along large parts to perform machining operations. The method is based on natural fiducials which are detected by a laser scanner and their identification in the computer-aided design file, without feature extraction. Once the usual requirements of the referencing of portable machines are studied, the method has been experimentally validated on a conventional three-axis milling machine to establish its accuracy, obtaining systematic and random errors and also its overall utility. The errors created by the experimental campaign have been studied and isolated, thus giving results that faithfully represent the proposed method. The results are compared with other state-of-the-art techniques to establish comparative accuracy values. Finally, the referencing method is expanded and integrated in an automatic working mode to operate portable machines and solve both local and distributed machining operations. To test this, the automatic method has been used to command machining operations in a conventional three-axis milling machine as it would be in portable machines to prove feasibility and overall validity.