How to Fill Holes in Wood:
Use vinyl spackling compound or water-based wood filler to fill small holes on interior surfaces. When applying wood filler, over fill the hole slightly to compensate for shrinkage as the filler dries. Once the filler has hardened, sand it smooth and prime and paint or stain, as desired.
Make your own wood filler by mixing sawdust or sanding dust with carpenter’s glue. If you plan to stain the wood, be sure to fill holes and cracks with stainable wood filler.
Use crayon-type filler sticks to fill holes and cracks on wood that’s already stained and finished with a clear topcoat. Choose a filler stick that closely matches the color of the wood. Overfill the hole slightly, then wipe away the excess filler with a clean cloth.
To fix large cracks and gouges on interior surfaces, use auto-body filler. Repair damage to exterior surfaces with two-part epoxy. Allow the epoxy to hardened overnight, then sand it smooth.
Patch holes in PVC trim boards with acrylic filler. Apply the filler with a caulking gun. Once the acrylic filler hardens, sand it smooth.
For More: How to Fix Rotted Wood With Epoxy; Exterior Wood Staining Made Simple