Thanks for your question.
Note: To automatically separate non-plated drills please view the following link, https://support.numericalinnovations.com/support/discussions/topics/14000003231
Yes, you can just "uncheck" any holes that are unplated (menu: Setup / NC Tools Table...)
Or manually select and place any drill holes on a separate layer (for non plated).
1. Using the selection Filter just enter the Tool #,
2. Or create a separate layer for non-plated drills, and then change the Layer Properties to the "non plated" drill layer.
Here's a quick tutorial video showing me manually place non-plated drills on a separate layer(no sound),
Thanks again and please let me know if you have any questions.