Use a putty knife to clear loose or rotting wood debris from the area to be filled. If the area is still damp after removing debris, let it dry thoroughly before applying Bondo.
Mix equal parts of Bondo resin and the hardener included with it in a disposable plastic container. Use a putty knife to knead the two materials together until they turn from brown to gray and form a putty consistency.
Fill the damaged area of wood with Bondo using a putty knife. Once the area is full, smooth the surface by dragging the putty knife across it at a sharp angle.
Let the Bondo dry for 24 hours to completely harden. Sand the surface of the Bondo smooth to match the surrounding wood.