A nanolithography method for altering the composition of supported phospholipid bilayers has been developed. Although a number of lithography procedures for various chemical systems currently exist, these methods typically rely on covalent bonding to stabilize the resulting structure. The, method described here is suitable for an entirely noncovalent system, where the pattern is maintained by specific hydrophobic and other noncovalent interactions. This lithography is achieved by the atomic force microscope, which is used to insert phospholipid molecules into a supported reconstituted high-density lipoprotein-phospholipid bilayer with 20 nm line widths. Lipid molecules are delivered to the supported bilayer through transient structural disruption, forcing the acceptance of new lipid monomers into the bilayer structure. Precoating the atomic force microscope tip with specific lipids is sufficient to deliver new lipid to the patterned areas. These results demonstrate a new method for controlling the structure of highly dynamic noncovalent surface assemblies.