I've done e-beam and UV microlithography on Si wafers with positive and negative resists. AFM lithography sounds like it is alot finer - moving around individual atoms, a bit like that famous photo of IBM written in atoms. My PhD was about designing the resist material to respond better to the e-beam, to give better sensitivity and contrast and finer details under e-beam. Is your field more physics or chemistry? I wrote a 0.1 micron line with a 10:1 aspect ratio with a e-beam in a negative resist.