In a few articles, I have come across images that are similar to SEM cross-sectional images but taken with AFM, but the article does not mention the details. Can you help me to measure in this way?
When referring to an article, it's always helpful to actually put the article in the question.
If you are talking about the cross-section of a cleaved sample, then the procedure would be equally straightforward and practically demanding: you cleave the sample in the region of interest, put it in upright on your AFM sample holder and measure the location of interest.
That sounds simple, but of course your sample holder must actually geometrically allow for an upright placement which is not the case for all models. Aside from that, if you're close to the sample edge, the risk of tip crashes is very high.
In our lab, we do an ion-slice on the cross-section. Then the topography is reduced to a minima. Then, e.g. different materials of the cross-section can be detected.