The higher thermal fluctuations of the atoms at room temperature introduces noise in the recorded AFM images thats why it is difficult to identify the single layer crystallinity. However, you can record the image with very fast scan speed (say around 30 line/sec) so that you can overcome the thermal fluctuations. After that remove the noise with FFT filtering and than you may have good atomically resolved AFM image
AFM is widely used for characterization of structures formed in MBE, for example: Si/Si Ge/Si islands of monoatomic height. AFM resolution in Z direction (perpendicular to the surface) is enough to resolve atomic steps dividing two neighbouring silicon layers of atoms (crystalline planes) and even domains of the superstructural reconstructions. In lateral X,Y directions AFM has worse resolution that depends on the cantilever characteristics. Acoustic noise and external electomagnetic fields are much more important for AFM measurements than thermal vibrations of atoms.
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