Prepare the surface by sanding the area with 220-grit sandpaper to remove any surface imperfections. Wipe down the wood with a tack cloth to remove the sanding dust.
Slip on a pair of chemical-resistant rubber gloves, safety goggles and a respirator. Mix water-based wood filler according to the package directions. The Family Handyman suggests mixing the two-part epoxy filler on an unwanted piece of cardboard or wood scrap. Use a tinted filler to repair colored wood or choose a basic filler to fix natural woods.
Apply the wood filler to the hammer marks with a putty knife. Apply slight pressure to the putty knife to work the filler deeply into the entire damaged area. Wipe away the excess filler with a damp cloth.
Allow the wood filler to dry for at least 12 hours, or until it feels hard to the touch. Remove the excess filler with 320-grit sandpaper. Work the sandpaper over the filler in the direction of the wood’s grain until the excess product is completely removed and the repair is flush with the surrounding wood.
Wipe down the wood window frame with a damp cloth or tack cloth to remove the sanding dust. Allow the wood to dry completely before painting or applying stain, varnish or shellac.