A review is given on recent developments of atomic force microscopic (AFM) studies on chemically reacting organic crystals. Three further basic phase transformation mechanisms have been added to the previous five. Both photodimerizations and gas/solid reactions are studied in detail by scanning the surfaces of initial and chemically reacted crystals of anthracenes, thiohydantoines, alpha- and beta-cinnamic acid, and stilbene at different faces, where technically possible. The AFM-features are correlated to known crystal structure data with the aid of semiempirical calculations in part. Thus, detailed molecular mechanisms far the far-reaching well-directed transport phenomena may be derived in most cases and the appearance of the submicroscopic features rationalized. Unimolecular terrace steps of anthracene behave as independent crystal face already. The addition of bromine and chlorine leads to new solid phases directly even though there might be formed mixtures of stereoisomers. If a submicroscopic liquid phase is formed as in the reaction of alpha-cinnamic acid with chlorine, the surface will be remodelled by the tip and this provides for interesting nanostructures. In many cases there are secondary phase transformations apparently from one form of mixed crystals into another form of mixed crystals either upon continuation of irradiation or just on standing of gas/solid reacted crystals for several hours.