Depends on how large they are. Really large ones, I try to avoid and sort out the wood. Very small one, I use CA glue or epoxy. For medium ones, I use epoxy, either plain or with a bit of saw dust from the same wood. That usually comes out a bit darker than the wood itself, so it depends on where it is and what it looks like. Sometimes I throw them away if the voids look ugly or cut them into spacers, a few I have put on my own knives when everything else was fine.
Ive been using a product called "Zap A Gap" from one of the knife supply houses. Its just a larger tube of CA, it is pretty thin, and soaks right in. Bigger voids need 2 or 3 applications to fully fill. Ive always used CA so Im not much help!
This how to, was provided by Stacy Apelt. He is a very talented blade smith I know from another forum.
Here is how I (Stacy) make all the pits, lines, open grain, and voids disappear on a handle.
BEFORE WORKING ON THE HANDLE OF ANY KNIFE, TAPE UP THE BLADE WELL TO PROTECT IT AND YOURSELF FROM UNWANTED INJURY.
A coat of Renaissance wax before taping makes the tape easier to remove, and keeps glue from getting under the tape as bad.
Some woods, like you koa, have a large and open grain, with some "cracks" in it.
Some woods, like stabilized redwood, buckeye burl, and most burls may be full of voids and large cracks/splits.
Some woods , like walnut, just never seem to get fully smooth,no matter how fine you sand.
Some woods, like black palm, are more like a bundle of rope than a grained wood.
How do you deal with these situations?
First, stabilized wood works and seals better than unstabilized, so getting problem woods stabilized is the first step. (On some of these woods, the problems come from the stabilizing .)
Next, you need to fill large openings with something that doesn't show much. For this, use fine wood dust and resin. When shaping the handle slide a cookie sheet under the sander and collect a zip-lock bag of sanding dust. When the handle is about 95% shaped and smoothed, mix up some slow set epoxy and make a thick putty with some dust. Put epoxy in the void to wet the surfaces, and then press/pack/rub in the putty. Apply it in such a way that you won't get an air pocket. Do all the voids and larger cracks and then set aside to cure for a full day. sand smooth with 220 grit and see what still needs attention.
Put on some rubber gloves, and put down yesterdays paper - the next steps get CA glue all over things.
If all the big voids are filled , now move to the smaller lines, splits, and cracks.If there weren't any in the handle start here.
Take thin CA and flood the crack with resin. Wipe off any excess quickly and immediately start sanding with 220 grit. Let the sanding work the dust created into the crack. After about 5-10 seconds of sanding, apply a drop more CA, and continue. In a few cycles, the crack will be filled, and may become difficult to even detect where it was.
Work the handle all the way around until all cracks/splits and pores are filled. Don't worry too much about the look of the finish yet.
Once the handle is sealed all over, wipe it down well with a rag dampened with acetone. Don't soak it, just wipe it clean. Set aside to dry and take a break for an hour or two. When back, look the handle over well. You may see some spots that missed detection earlier. Fill them and let cure for a couple hours again. Once satisfied, sand the handle to about 98% done, going up to 400 grit. Wipe off any dust and you are ready to do the final seal and finish.
Holding the knife vertically - blade upward- flood the entire handle with thin CA. Rub it into the wood a bit and hang in that position for about three minutes. Take a paper towel and wet it with acetone. Wipe the handle off until most of the excess CA is wiped away. Let dry for five minutes. Sand the handle lightly by hand with 400 grit paper until it is smooth and no CA "puddles" show. Repeat this about ten times, and the handle will get a smooth and seamless surface. Once done to a "Glassy" smoothness, work up the grits to about 2000-2500 grit. At this point the handle should shine and be flawless as far as and surface defects. A very light buffing with a new buff and white rough can make it super shiny - some like that some don't.
What makes sealing and filling the voids with wood dust and CA most impressive, it that the filled areas end up looking like natural grain lines, knots, and spalts.
Toss all the bags of dust in a box ( label the bag with the wood type) and use these to make repairs as needed in future projects.
Lets say you accidentally drilled a rivet hole wrong and it came out the other side crooked......or it is in the wrong place......or you ground too deep in the palm swell area and cut into the tang hole down the center of the handle!!! We all do these type of things. If the wood is not easily changed, or too valuable to scrap, try making a knot. Use the Dremel to dig out an irregular shape the seems right for a knot or other feature. Make it as deep as practical, with undercut sides - to lock the filer in strongly. Using a appropriate color of wood dust, make a putty up and fill the hole. If the flaw is tiny, you might get away with using the same wood color, but normally ,a darker shade looks like a knot or natural wood feature. Let cure well and sand down flush. Now you can re-drill the hole and/or continue the handle finishing.