The energy dissipation of different phases of PTCDA (3,4,9,10-perylene-tetracarboxylic-dianhydride) on Ag-Si(111) √3×√3 was investigated by means of atomic force spectroscopy using a custom-built low-temperature atomic force microscope (LT-AFM). The energy dissipation is due to non-conservative forces between the tip and sample. We present preliminary energy dissipation data measured when the tip was placed above four different PTCDA superstructures. While one of them showed energy dissipation, the others did not. The dissipation process seems to be critically influenced by the junction geometry; a chemical bound between the tip apex and a specific site of the molecular layer might be one channel for the dissipation. [DOI: 10.1380/ejssnt.2011.21]