Visualization of atomic structure using AFM: theoretical description
  We suggest simple model of image formation in atomic force microscope (AFM) taking into account contact deformations of probe and sample during scanning. The model explains the possibility of AFM visualization of regular atomic or molecular structure when probe-sample contact area is greater than an area per atom or molecule in surface lattice. (This is usually the case when lattice to be studied has subnanometer unit cell parameters and AFM investigations are carried out in air in contact mode). Two special peculiarities of AFM visualization of two-dimensional lattice could be observed under such conditions: 1) the inversion of contrast of AFM images, and 2) visualization of "false atom" under single atomic vacancy of surface studied. 
M.O. Gallyamov, I.V. Yaminsky
cond-mat.mtrl-sci