Sand Paper, approximately 1000 grit (found in automotive sections for car detailing)
Rubbing Alcohol (optional)
Whenever possible, I wet sand. I take the doll over to the sink and run the water and either douse both it and the sand paper (if I'm removing all the makeup) or I keep a small piece of sandpaper wet and use that if working on a particular area. Wet sanding yields smoother results, and leaves both your doll and your sandpaper cleaner (it also makes your sandpaper last longer). Wet sanding is not such a good idea if you are removing portions of makeup on a doll that has already been partially customized and hasn't been sealed with waterproof sealant for obvious reasons.
Sanding: (If you've ever done fine sanding work you canskip this paragraph). Generally the best method from jewelery making to furniture construction is to start with a rougher sandpaper and work your way up to fine. I start with 800 grit sandpaper or something thereabouts, and use even pressured circular motions over the area that I want to sand. If you are working on eyebrows and do not want to disturb eyeshadow, or vice versa, you may want to use a finer sandpaper and use lighter smaller strokes to have better control. If there are any areas that have light scratches from the sandpaper, you can smooth them out with the higher grade sandpaper.
Onto the face: If you are removing all the makeup, you might want to open up the head and remove the eyes first. Why? Because you won't damage the eyes accidentally this way, and you won't accidentally break the neck (more of a risk in type 1 dolls).
Start anywhere. Just make sure to do a thorough job, even sanding areas that do not need to be sanded for an even finish.
If you are going on to matte the body as well, take the body apart as well as you can and sand each piece individually before reassembling it. Once again, this is so that you can easily get into all the nooks and crannies and not worry about breaking anything.
And that should take care of it! Sanding is the easiest part. Type 1 and 3 bodies can do with sanding to help them match the face, and early type 2 bodies (Arietta, Venus) can have their arms and legs matted to make them match the soft torso better.