1.1 Tip-sample convolution
This is an inherent feature of AFM and can never be fully removed. Any AFM image is a convolution of the shape of the probe, and the shape of the sample. This has the effect of making protruding features appear wide, and holes appear smaller (both narrower and often less deep, too). Broader (less sharp) probes will enhance the effect, as shown below.
Illustration of convolution of AFM probe and sample giving rise to the image (red).
Probe-sample convolution tends to have the greatest effect on features of similar or smaller radii than the probe. it can be reduced by deconvolution techniques, discussed further in "Atomic Force Microscopy".