Remove the plywood countertop with a pry bar and a hammer. Pry it up from the base cabinet. Work slowly and gently to avoid cracking the wood.
Examine the plywood sheet. If the bottom is still serviceable and the top is very marred, you can simply flip it over and use that side after refinishing it. If the top is only slightly marred, it can be sanded down and refinished, as well.
Sand the plywood with a hand sander. If the plywood is under a 1/4-inch thick, use a hand sanding block instead. Use a medium-grit sanding pad or block to start. This will remove the old finish and smooth out any scratches. Remove all the dust with a vacuum and tack cloth. Re-sand the surface with a fine-grit sanding block.
Stain the surface of the plywood with wood stain. You can use a stain applicator or a paintbrush, whichever you prefer. Apply a light coat of stain. Let it dry for four to six hours. If this is the desired color, you are ready to move to the sealing process. If not, sand the surface lightly and apply another coat of stain. If you will moving on to seal the wood, sand the surface lightly before you start.
Apply one coat of polyurethane to the wood. Use a paint brush and go with the grain of the plywood. Apply a thin coat and let it dry completely, usually between six and eight hours.
Check for any imperfections in the finish. Look at the finish. If you see any bubbling, sand the area down and apply polyurethane to the area. If it's fine, you are now ready to reattach the countertop.