First, I take an xacto knife and score alone the eyes where I want to cut them out. After that, using the xacto knife, I start to bore a hold in the middle of the eyeball until I get through it. Gently, I cut and scrape away all the clay to the scored lines. If you have an open mouth doll, the mouth is next. Score in the same way as the eyes and then use cuts to get through and cut and scrape away the excess.
Some people just paint in nose dots at a later time.
When this is all done, scrape and smooth away the seam lines with an xacto knife. I either use my thumb or a piece of nylon stockint to finish smoothing them out. Don't scrape too low or you will have a flat place instead of the rounded contours. When this step is finished, I check the whole piece for any imperfections and then smooth them out. Use a soft brush to smooth the mouth and eyes.