I'm working on a tabletop right now. It's Bigleaf Maple, and it's got a few surface defects like small cracks in knots, and beetle tunnels. These are part of the natural beauty of the material, but on a dining table, little holes will just fill with gunk.
So I filled them with clear 5-minute epoxy, which was really easy and preserves the look. The finish on this top is simple: a couple of coats of Watco Natural to pop the figure and bring out depth, followed by a topcoat of oil-based polyurethane varnish for durability. I was concerned that the epoxy might fill the pores around the defects and change the way the finish looked, so I tested doing the Watco first, then the epoxy, then re-applying the Watco where I scraped and sanded around the repair. I also tested simply putting the epoxy on the raw wood before even doing my final surface prep.
The latter is much easier, and worked fine for me. At least with these finishes, and, more importantly, on this smooth, closed grain wood, the epoxy is too thick to really soak in and cause problems. If I were working in oak or something similar with a lot of big pores, I'd probably do a prefinish step. This process also becomes much more difficult if you're going to stain and want the defects to blend in. In that case, you can try coloring the epoxy with a small amount of dye or paint pigment (go darker than you think) or try pre-staining and filling over it.
Here's what I did. I got a tube of 5-minute epoxy at the hardware store. Common stuff. Squirt out a bit into a plastic cup or onto a piece of scrap, and mix it slowly but thoroughly. Try not to get many air bubbles, because they'll show up in the filled hole. You can see a few in the second photo after I scraped it down. Dab the epoxy into the voids, working it down with a toothpick or similar so it makes good contact with the inside surfaces, and leave it very proud of the surface everywhere. You don't want to have to try to come back and fill a little shallow depression because you didn't use enough. Work quick. If you mix it right, it will start getting thick and stringy in... (spoiler alert!) about five minutes.
|Overfill the holes. It's easy to scrape off later.|
Let it cure for at least a few hours. It shouldn't feel sticky or leave any dent when you press on it. Now it's time to shave it down to the surface. I usually start with a sharp block plane, but you can use a chisel if you're careful. Just shave off thin slices. Don't try to remove the whole bump at once, or you might just pop the entire patch out of the hole, especially if you applied an oily finish first. Once you get it down pretty close, get the card scraper out and continue gently shaving until you've removed all the excess and are just biting into the wood all around the patch. You can also try a stiff sanding block, but a flat scraper does a much better job because the epoxy is inevitably tougher than the wood and you run the risk of sanding a divot around the patch trying to get the last bits of epoxy off.
Then I do my final surface prep. In this case, I used a random-orbit disc sander and some 150 grit paper over the entire top before applying the Watco.