As others have mentioned (assuming those are blind holes), you'll want a bottom tap, or "bottom" thread chaser.
I've seen a few of those, but always as taper taps, never as a bottom tap.
If you don't want to make your own thread chaser, and don't want to remove any material, maybe a used, worn, and very dull 8-40 bottom tap would work? (Usual precautions, don't break it, etc.)