Atomic force microscopy: depth penetration?
Taken right from the Wiki page you linked to:

AFM only images the surface of a specimen, to a maximum depth of 10-20 &micro;m and a maximum scan area of 150 &micro;m x 150 &micro;m. Compared with scanning electron microscopy, SEM has a much larger depth of penetration and scanning area (~1 order of magnitude greater). AFM is also a much slower scanning method.