Scanning Tunneling Microscopy (STM) is a very powerful technique for studying surfaces. STM is capable of producing true atomic resolution information and under the right conditions can directly reveal the location of surface atoms themselves. Further the information gained is in real space, which means that often it is very intuative to interpret.
STM is a remarkably simple technique for the power it gives. In general terms an atomically sharp conducting tip (normally tungsten) is brought close to the surface of interest and a voltage is applied between the two. The tip and conducting surface, although not touching, are close enough that a quantum mechanical tunnelling current (of the order of a few nanoamps) can flow between the two. The magnitude of this current is exponentially dependent upon the tip-surface separation. If the tip is then moved in the plane above the surface then any slight undulations causing the surface to move closer to or further from the tip will cause a much larger change in tunnelling current. In practice the tip is moved in a raster like pattern across the surface and it’s "height" adjusted to maintain a constant tunnelling current. The height of the tip therefore maps out the surface and a picture can be built up of the area scanned. This is normally represented as a grey scale image, with the grey scale representing tip height.
There are a few useful STM sites available on the web: