This video shows CNC planing a piece of MDF. Although the MDF is already flat, it is not perfectly level with the machine.
Planing a thin (1mm) layer off ensures that the new flat surface is perfectly square with the cutter, so subsequent operations will be the same depth across the entire surface.https://www.youtube.com/watch?v=YgszXhNi2yg
This used a 32mm diameter cutter with two flutes. Shank size 12.7mm (half inch).
Cutting depth was approximately 1mm - just enough to ensure the slight misalignment of the machine base compared to the cutter was eliminated.
The fixed base of the machine varies by about 0.5mm across the total width - very little, but when engraving to a depth of only 1mm, enough to totally ruin the finished engraving.