Mixed monolayers of dimyristoylphosphatidylcholine (DMPC) and quercetin palmitate (QP) in a molar ratio of 25/75 have been transferred on mica and oxygen plasma cleaned silicon by the Langmuir-Blodgett (LB) technique at different subphase temperatures. Scanning Force Microscopy (SFM) in height, phase and lateral force modes has been employed to investigate the structural and mechanical features at nanoscopic level of these samples. Although the two molecules show a wide range of miscibility at 37 °C, they give rise to phase separation at 10 °C. This last system provides a new example of nanometric scale self-organization. In particular spiral shaped domains rising from the wrapping-up of nanoscopic fiber-like structures have been observed. The high resolution achieved by the use of the dynamic scanning force microscopy operating in the net attractive regime allow to visualize characteristic nanoscopic rupture points along the supramolecular fibers. High mass resolution Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) spectra showed DMPC- as well as QP-related peaks. The ToF-SIMS spectra from the nanostructured samples (10 °C) have been compared with those from the homogeneous ones (37 °C). The phase separated samples provides interesting secondary ions that highlight the QP supramolecular condensation within the fiber-like structures.