Note that for home etching, you probably do NOT want the holes etched. Or at least, you want much smaller holes etched. If you etch a hole the size of the drill, and the drill is off, you end up with the copper not touching the edge of the hole. In PCB there's a "drill helper" option that tells it to etch a small hole (about 10 mil) at the center point to help you center the drill bit, but not big enough to cause problems with off-center holes.
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Re: [Homebrew_PCBs] drill holes in gerber file -how can it be done
2008-08-08 by DJ Delorie