During the past 20 years, the manipulation of atoms and molecules at surfaces has allowed the construction and characterization of model systems that could, potentially, act as building blocks for future nanoscale devices. The majority of these experiments were performed with scanning tunnelling microscopy at cryogenic temperatures. Recently, it has been shown that another scanning probe technique, the atomic force microscope, is capable of positioning single atoms even at room temperature. Here, we review progress in the manipulation of atoms and molecules with the atomic force microscope, and discuss the new opportunities presented by this technique.