My screwed insert came today. So I did let the CNC drill all 309 holes with a 6mm drill bit.

Then I started to drill the holes for the screwed inserts with 8mm by hand. I noticed that the wood starts to split when I used the 8mm drill bit directly. So I used countersink drill bit first with the diameter of the head of the inserts.

So every 2nd hole (82 holes) has an insert that provides an M5 thread to bolt down things. And the other holes will be used with simple wood dowels to provide a fixture for x and y axis.

I guess when I am done with the inserts I will use some sandpaper to smooth the surface again.