Yoshiaki Sugimoto at Osaka University in Japan, and colleagues, have devised a way to discern not only individual atoms but also their chemical identity using an atomic force microscope at room temperature according to an article at NewScientist.

NewScientist includes a photo of individual tin, lead, and silicon atoms on a surface color coded blue, green, and red.  Very cool.

The microscope works by measuring how much the atoms attract or repel the pyramid shaped tin tip of the atomic force microscope.  The strength of that force varies as the distance from the atom varies and that relationship is slightly different for each type of atom.