and not powderpost beetle exit points, or exidence of some other wood eating pest;
it depends on if you're painting, staining or just filling these holes.
If the wood is already stained and finished, minwax and other wood finishing supply companies have filler sticks that you can use to match the finish and just "smudge fill" in.
If you're planning on stripping and then re-staining these areas, do ahead and do that then use those sticks to fill AFTER you stain but before you top coat with clear finish, as any wood filler will NOT take up the stain and the "filled" areas will stick out like a sore thumb.
If you're going to paint, you can go the "cheat" way or the right way. The cheat way is to sand a bit and fill with painter's caulk then let dry/cure, then paint overtop. The right way is so sand/strip down, wash, fill with wood putty, sand, prime, de-gloss sand, then paint.
Hope that helps. Oh, NEVER use "spackle" or any wall patching material to "fill" it will look awful in no-time.