Putting masking tape on a finished body, marking hole positions on that and drilling through the tape is a good way to drill holes at the very end. The tape can also help stop the finish from cracking/splintering, though using sharp drill bits should prevent that. It can also be a useful way of drilling holes before finishing, especially if you need to draw lines to line things up first and don't want to mark the wood and then have to sand off the pencil lines.