Aggregates of oligonucleotides and the surfactant, CTAB, have been studied with force spectroscopy using an atomic force microscope. Gold coated AFM tips were derivatized with long carbon chain thiols and thiols functionalized with carboxylic acid and amine head groups and used to measure the strength of interaction or adhesive force between the AFM tip and aggregate surface. Force curves were obtained at various locations on the aggregate surface showing consistently reproducible adhesion within a given spot and some variability in adhesion from one spot to another. Adhesive forces were also measured in the same way on a model system composed of self-assembled monolayers (SAMs) formed using the thiols mentioned above on gold coated silicon wafers for comparison. Forces of attraction between the derivatized tip and the model SAM surface were quite a bit lower compared to measurements made on aggregates. Some force curves obtained from aggregate surfaces showed broad retraction traces indicative of a strong adhesive force that may include a cascade of detachment steps. Currently, friction (lateral) force experiments are underway on both the aggregate surface and the model system to determine the surface free energy between the tip and surface and the extent of homogeneity on the aggregate.