It's been a while, but...
The ribbed strips which sit on top & inside the rails can be pried out with a flat-bladed screwdriver. You'll find fasteners concealed within. There are also a few fasteners under the luggage rack's "wing" which allows you to separate it from the rails, but they're easier to deal with after the rails have been removed.
I
think there are also some nuts which have to be removed from the underside of the decklid.
Filling the holes & having the plugs last without shrinking or cracking is a bit of an art form.