Crystals of hexamethylenetetramine (HMT) with aliphatic dicarboxylic acids in 1:1 molar ratio exhibit different behaviour depending on the number n of carbons in the aliphatic chain. For n=8 and 10, incommensurate phases have been observed, while for n=9, a commensurate disordered phase is found. The structure consists of alternating layers of roughly spherical HMT and acid chains. Atomic force microscope (AFM) has been used in order to characterise these layers in several different crystals. Images have been collected in contact and tapping modes. Contact mode images reveal that the tip interaction removed systematically an integer number of layers of the crystal. Morphological changes of the surface are observed in the images collected in tapping mode.