Probe-based methods for patterning a surface of a material are described. In particular, high resolution patterning of molecules on a surface of a material, such as nano-scale patterns with feature sizes of less than 30 nanometers, are described. In one aspect, a method for patterning a surface of a material includes providing a material having a polymer film. A heated, nano-scale dimensioned probe is then used to desorb molecules upon interacting with the film. The film includes a network of molecules (such as molecular glasses) which are cross-linked via intermolecular (noncovalent) bonds, such as hydrogen bonds.