Self-assembling aromatic dipeptides are among the smallest known biological materials which readily form ordered nanostructures. The simplicity of nanotube formation makes them highly desirable for a range of bionanotechnology applications. Here, we investigate the application of the atomic force microscope as a thermomechanical lithographic tool for the machining of nanotubes formed by two self-assembling aromatic peptides; diphenylalanine and dinapthylalanine. Trenches and indentations of varying depth and width were patterned into the peptide tubes with nanometer precision highlighting the ability to thermally machine and manipulate these robust and versatile nanotubes.