Creating patterns of microstructured arrays of functional material is of interest in many areas of current surface science and microsensing techniques. We have used the atomic force microscope to create micrometer-sized structures of poly L-lysine on lipid bilayers. The entire process was performed in aqueous solution. The created structures were 0.8 +/- 0.1 nm high and as small as 100 nm in diameter. Our results suggest that at least part of the poly L-lysine molecules in these structures are anchored to the mica surface below the lipid bilayer. Thus, the presented method might also be used to design structures of poly-L-lysine and other biomolecules on mica.