In Mach3, go to the Settings Tab, and select "Set Steps Per Unit". It will ask you how far to move the machine. Before you do this, make a mark on the table exactly where the end mill is resting. You can do this by lowering the end mill until it touches the material, then spinning it by hand to cut a small dimple in the material. Then, raise the end mill to clear the material, and assign a distance to move the machine. Once the machine moves and stops, measure the exact distance that it actually traveled with a tape measure, and enter this value into the dialog box that asks how far it moved. Mach3 will automatically adjust your steps per unit for that axis to be more accurate. Do this for all axes often to ensure you are cutting accurately. The longer distances you use calibrate, and the more precise you are with your measurements, the better.
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What is the best way to calibrate my machine?