I realise this is an insult to most builder’s intelligence and for this I truly apologise. When cutting the V-Slot extrusion / rails it is paramount that the important ends are perfectly square and true. Check them with a square and if necessary correct any error by light machining or even some extremely careful hand filing. Likewise when assembling the machine frame all the V-Slot should be square, parallel, plumb and true as appropriate. Taking the extra time to get the frame dimensionally accurate at an early stage will pay dividends later on when it comes to operating the finished CNC machine and of course, it will be evident in the quality of the work the machine can produce. The following illustration is just a gross exaggeration of the problem that can be caused if the ends of the V-Slot are not exactly square and true. Tweakie.
