A method of determining a positioning error of a CNC machine is provided and an system thereof. A calibration element is placed within the CNC machine. A first sensor reading is taken of the calibration element. A second sensor reading is taken and the sensor is moved in a manner that the difference between the first and second sensor data decreases until the difference becomes less or equal to a pre-determined threshold value. A positioning error of the tool head is determined based on the movement of the sensor.