We report on the morphology evolution during heating and melting of lamellar poly(isoprene)-block-poly(ferrocenyldimethylsilane) (PI76-b-PFDMS76) raft crystals deposited at the native oxide surface of silicon (SiO2) or at a highly ordered pyrolytic graphite (HOPG) surface, studied by in situ temperature controlled atomic force microscopy. Crystals deposited on hydrophilic SiO2 surfaces revealed an irreversible decrease in length at temperatures of up to tens of degrees above their expected melting temperature, while maintaining their platelet-like structure. Crystals deposited on hydrophobic HOPG surfaces initially decreased in length below their expected melting temperature, while at 120 °C and above a typical molten morphology was observed. In addition, the irreversible formation of a PI76-b-PFDMS76 wetting layer around the crystals was observed upon increasing the temperature. These observations in the morphological behavior upon heating emphasize the role of interfacial energy between a surface deposited block copolymer based macromolecular nanostructure and its supporting substrate.