We have studied the surface morphology of free standing single crystals of thermochromic polydiacetylenes (PDAs), namely, ETCD and IPUDO (respectively, the ethyl and isopropyl urethanes of 5,7-dodecadiyn-1,12-diol), by Atomic Force Microscopy (AFM) under ambient conditions. Micron scale as well as molecularly resolved images were obtained. The micron scale images indicate a variable surface, and the molecularly resolved images show a well defined 2-D lattice that is interpreted in terms of molecular models and known crystallographic data. Thereby information about surface morphology, which is crucial to potential optical device or chromic sensor performance is available. We also report the observation of a “macroscopic shattering” of the IPUDO monomer crystal during in-situ UV polymerization studies.