Brian, there are clear pore fillers and colored pore fillers. The latter is generally used for effect when you want to accentuate said pores. While you "can" apply them over the bare wood, it's somewhat normal to seal first (after any oiling, etc) with de-waxed shellac so that any coloration in the pore fillers do not stain the wood. After they are cured, another application of de-waxed shellac seals the filler and provides a good base for whatever finishing regimen you intend to use beyond that point. There are both water based and oil based fillers. The latter is a little easier to work; the former dries out pretty quickly so you have less time to level it with the plastic spreader and work it with burlap, etc.