I would recommend watching him next time he is let out to determine if any scratches are on purpose or accidental. Some cats will use wood to scratch, but I've never seen cats use wood that's finished and sealed (as I assume your floors and countertops are). So, it COULD be on purpose, but I suspect it's accidental.
If it is on purpose, the same type of advice applies whenever you want your cat to stop purposefully scratching anything. Give your cat a surface of similar texture/shape/weight/etc and treat it with catnip to act as an initial attractant. These considerations are covered in "How can we prevent our cats from scratching on our chair?"
If it is accidental, there are a few ways that you can to reduce the damage to your surfaces.
First, you can dull his claws by trimming or applying nail caps. This will ensure that if he tries to grab the surfaces, his claws are not able to damage the wood.
Second, you can observe him to see if there are certain spots where he tends to have these accidents, and put rugs with rubber gripping bottoms in those spots to give him more traction. For example, when our cat Hunter was younger he liked to jump on top of a tall wardrobe we had, but to get up there he had so much momentum that we were worried that he would fall off the other side! We bought a cheap bathmat to put there to give him a safe "landing".
Finally, if the finish on the wood surfaces is old and worn, you can resurface them. Then the protective layer will be thicker, and your cat will be less likely to damage the wood through it.