ABSTRACT This study proposes a reconfigurable open architecture control system for the Computer Numerical Control (CNC) woodworking educational machine tool called “EMCO F1 CNC”. On this machine physical hardware reconfiguration (spindle position can be vertical and horizontal) is possible. The idea was to develop a control system that would follow the configuration changes of the machine tool. The educational character of the machine and its reconfigurability demand possibilities for machining programme simulations in order to determine optimal workpiece position in the workspace and programme verification. Those are the reasons for developing a virtual machine tool integrated with the control system as a digital twin. The study presents a novel methodology for the development of control systems, merging the concept of “virtual commissioning” with iterative error-driven processes. The objective was to develop a dynamic control system capable of promptly adjusting to kinematics changes in real time. In a wood machining experiment, a test workpiece for machine tools for both machine configurations verified the operation of the developed control system.