Nor do you want to mill into your precision paralles. If you place them judiciously under the plate to avoid the cutter you will be ok but it is always good to have some sacrificial parallels around. Do the T-Nuts in your clamping set fit into the T-Slots of your bed? Sometimes they stick in the bed slots and you have to file or grind the sides of the T-Nuts down a bit. Do not mill them as they are case hardened and will burn up your endmill cutter.