Sand it down a little with nothing less than 1000 grit sandpaper. Go to your local auto parts store, they generally carry fine grit "automotive grade" sandpaper in the same isle as their body repair and paint stuff. After you do that, make sure you burnish the shaft to close the wood pores. I went to a local leather works shop and asked them for a scrap piece. They gave me a big bin to pick from, make sure you get a raw leather (undyed) piece. Using the suede side, stroke it up and down the shaft until you can feel heat. The heat from the friction will close the pores in the wood. I never put any kind of sealer or wax on my shafts, I prefer the natural wood feel. If you can't get a piece of leather, a brown paper bag (like a grocery bag), or a crisp dollar bill will suffice.
Maintaining a clean shaft is really easy as well. When I'm all done playing, I wash my hands. I take the paper towel I used to dry my hands off, and I stroke the shaft with it to remove any oils my hands left on the shaft. I then take the same paper towel and wipe the chalk off the tip of my cue, to keep the chalk from getting inside my case and bluing my shaft.
Hope this helps.