How does acetone remove pencil marks?
Pencil lead writes on rough surfaces by abrading into tiny particles and getting pushed into surface irregularities. If the surface isn't rough, you would get no visible residue of graphite. A pencil might sometimes even leave a scratch on dense wood that is so smooth that it has almost no blackness from graphite.

Wood is hydrophilic and even contains some water (unless bone dry). Graphite is not so hydrophilic or polar. Acetone wets the wood surface and either swells it by diffusing into watery regions or simply gets between a graphite particle and the wood surface, loosening any van Der Waals forces holding the graphite to the wood. While the surface is wet, the graphite can be wiped off (or smeared out so much that the original mark is not visible any more). Then the acetone evaporates quickly and the wood looks clean(er). Ethanol or isopropanol might do as well - even water (especially with a surfactant to coat and disperse the graphite) might work. 

A grease pencil would be much more difficult to remove because so much material is pushed into crevices that a solvent can't easily loosen it without spreading it.