Leveling the wasteboard is something that should be done to make your CNC leveled, MDF is not a perfect material and can move with humidity, however, I would recommend that you do this to the secondary wasteboard. Did you install a secondary wasteboard that you can damage if the bit goes through, where you have something to attach your hold down clamps? When it gets damaged, gouged or out of level, you can reface it again. I use the Whiteside 6210 CNC Spoilboard Surfacing Router Bit, 1/4" Shank that you can find on Amazon to perform this task. It is much faster and provides a better finish than trying to do this with a 1/4in endmill. You run a thin (probably 0.1in) pocket toolpath for the whole surface of your wasteboard.
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