Photolithographic methods are useful in patterning SAMs.  SAMs are also useful in depositing nanostructures, because each adsorbate molecule can be tailored to attract two different materials. Current techniques utilize the head to attract to a surface, like a plate of gold. The terminal group is then modified to attract a specific material like a particular nanoparticle, wire, ribbon, or other nanostructure. In this way, wherever the SAM is patterned to a surface there will be nanostructures attached to the tail groups. One example is the use of two types of SAMs to align single wall carbon nanotubes, SWNTs. Dip pen nanolithography was used to pattern a 16-mercaptohexadecanoic acid (MHA)SAM and the rest of the surface was passivated with 1-octadecanethiol (ODT) SAM. The polar solvent that is carrying the SWNTs is attracted to the hydrophilic MHA; as the solvent evaporates, the SWNTs are close enough to the MHA SAM to attach to it due to Van der Waals forces. The nanotubes thus line up with the MHA-ODT boundary. Using this technique Chad Mirkin, Schatz and their co-workers were able to make complex two-dimensional shapes, a representation of a shape created is shown to the right.
Another application of patterned SAMs is the functionalization of biosensors. The tail groups can be modified so they have an affinity for cells, proteins, or molecules. The SAM can then be placed onto a biosensor so that binding of these molecules can be detected. The ability to pattern these SAMs allows them to be placed in configurations that increase sensitivity and do not damage or interfere with other components of the biosensor.