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Complex molecules and biomolecules can self-assemble and self-organise in mesoscale structures with typical sizes from a few nanometres to several micrometres. Such structures have great potential for many applications ranging from micro/nanopatterning and chemical sensor technology to biomedical implants and targeted drug/gene delivery. The atomic force microscope has played a critical role in recent advances in the nano/microscale analysis of such systems and generally in the development of the field of soft nano/biotechnology. No other instrument is so versatile to be able to measure the structural, mechanical, frictional and adhesive properties of soft structures in dry state and within liquids with a spatial and force resolution at the sub-nanometre and sub-nanonewton scale, respectively. In this talk, I will present examples of its use in investigations of various soft matter and biomedical systems including: amphiphilic diblock copolymers, graft copolymers, polymeric and phospholipid-based biomedical microbubbles.