Good day, I thought I would ask for guidance from anyone who has faced this. I used a clearance tool to remove the excess material. Can you see where the depth of the cut is different as it is moved through the removal process? It does this no matter what part of the table I work from. I did another surface but on the table but I am still getting this. It is almost like each cut it takes is a different depth. Has anyone had this issue?
You might want to explain exactly what you are trying to cut. It looks like you're just trying to cut out some letters. If that is your goal, you only need to do a profile cut and not worry about the clearance tool. You can even use a V-bit to do the profile cut. I do it ll the time. If you want, you could apply some tabs so the letters won't move on you and possibly damage your project. If I am not understanding what you're trying to do, please try to be more exact and others will also try to assist you.
If you're really using a down cut bit for clearance I would suggest converting to an up cut to get better chip evacuation and eliminates the risk of starting a fire. If you're using an up cut bit while telling the software it is a down cut then if the work isn't rigid and can flex up that would explain varying bottom height and taking lighter cuts may help. If your machine's Z axis were skipping steps it would have a rough bottom but likely just keep getting shallower or deeper instead of going up and down.