The use of Atomic Force Microscopy (AFM) to investigate the effect of different annealing temperatures on the selfassembly properties of Iron (III) oxide nanoparticles prepared by the Langmuir-Schaefer method is experimentally demonstrated and discussed. Ferritin molecules containing a self-assembled core of iron oxide undergo thermal treatment to produce the nanoparticles. When the Iron (III) oxide nanoparticles were subjected to annealing temperatures, they were found to coalesce especially at the boundary of the graphitic substrate to conserve energy. At higher temperatures the particles were again seen to coalesce more, forming islands at the graphitic boundary. Further studies revealed that these islands represented different phases of Iron (III) oxide nanoparticles that resembledγ-Fe2O3, α-Fe2O3and a third phase that likely was a combination of γ-Fe2O3 and α-Fe2O3.