You can use a card scraper or sand paper to remove the excess powder from the surface of the wood. I prefer using a card scraper because it can quickly level the surface, and will provide a cleaner finish to the buttons. Sandpaper works fine, but the surface of the metal will not be as brilliant as a scraped surface. That being said, it is much more difficult to prepare & use a card scraper, so sanding is probably a safer choice if you have never used a card scraper.
There are plenty of resources available on line for preparing the edge of a card scraper and learning to use it, but that is out of the scope of this guide. Check out this video from Brian Boggs if you would like to learn more.
Once the surface of the button has been leveled with the wood, you are done! If you would like, you can use a fine coat of your favorite wood finish to seal the wood. The finish will not interfere with the sensitivity of the buttons.
You can now refer to the MPR121 guide to learn how to connect the button to your Arduino!