Tunable nanostructures can be patterned in Ga[Al]As heterostructures with an atomic force microscope (AFM). Oxidizing the GaAs cap layer locally by applying a voltage to the AFM tip leads to depletion of the electron gas underneath the oxide. Here, we describe this type of AFM lithography as a tool to fabricate tunable nanostructures and characterize the electronic properties of the resulting confinement. As an example for the versatility of this technique, we present conductance measurements on a quantum wire as a function of its position. Conductance fluctuations in real space with a characteristic period of 2 nm are observed and interpreted in terms of individual peaks in the potential landscape the wire hits as it moves through the host crystal.