Nanostructures of lysozyme molecules adsorbed to mica were generated by the tip of an atomic force microscope in contact, tapping, and force-distance mode in aqueous solution. In contact mode at high ionic strength and adjusted lysozyme concentration a monolayer of defined pattern and orientation could be formed by the scan process of the tip. A lysozyme monolayer with minimal pattern size of about 60 unit was achieved by line scan. At larger loading forces besides a monolayer also 3D-aggregates of lysozyme molecules could be generated. In force-distance mode the volume of 3D-aggregates grows with increasing generation time, lysozyme concentration in the bulk phase, loading force, and frequency of up- and down-movement of the substrate toward the fixed cantilever. In tapping mode 3D-aggregates could be generated as well. It is postulated that reduction of electrostatic interaction between the oppositely charged lysozyme molecules and mica surface by sufficient high ionic strength is essential for monolayer formation. It is discussed that for the underlying mechanism of monolayer generation in contact mode lysozyme molecules of the bulk phase adsorb to the tip, become pulled off and attach to the mica surface by the scan process of the tip. (c) 2006 Elsevier Inc. All rights reserved.