When 10,12-pentacosadiynoic acid ( PENTA), dissolved in phenyloctane, is brought into contact with graphite, it immediately builds a film on the surface. The molecular arrangement of this ordered film has been characterized with an STM. The same packing was observed in a PENTA 2D-domain adsorbed from the solution into a small artificial hole scratched with an STM tip in a perylene- 3,4,9,10- tetracarboxylicdianhydride ( PTCDA) layer formed in advance by vacuum- deposition. Thereby, a nano- scale domain of diacetylene molecules is embedded in the PTCDA film. In the posterior imaging scans, the original irregular scratched area becomes regular due to the readsorption of PTCDA into the gap.