Drill the hole slightly larger and install a plug cut from the same
wood species.  Orient the grain with the surface.  A 1/4" plug usually
is sufficient unless the holes are larger, in which case you'll need
a larger plug cutter.

Cut the plugs and let them cool, then use a thickness gage to measure
their ultimate diameter.  The bore might need to be a few thousandths
smaller than the plug cutter designation.  This will insure a snug fit.

The plug does not need to be the length of the piece being filled.
Leave it a little higher than the surface and trim with a flush cutting
saw or razor blade.  If you're using a chisel or razor blade, start at
the top of the plug to see how the grain runs.  You don't want to have
the plug break below the surface due to the grain running down; trim
in the grain upwards direction.

Jon Page
Harwich Port, Massachusetts