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You can do all sorts of fancy chemical vapor deposition and lithography, but until you take a look at your result with a microscope, you're running blind.
I can't stress enough how important microscopy is to nanotechnology. All of our synthesis efforts would be in vain if we couldn't characterize them. The only reason we know that carbon nanotubes are actually hollow tubes, is because someone looked at it through an electron microscope and discovered it.
There are two main kinds of microscopy. The first class of microscopy involves a stationary sample in line with a high-speed electron gun. Both the scanning electron microscope (SEM) and transmission electron microscope (TEM) are based on this technique. The second class of microscopy involves a stationary scanner and a moving sample. The two microscopes in this class are the atomic force microscope (AFM) and the scanning tunneling microscope (STM).
Before I get into this, let me just say this: the differences between the four microscopes are huge. The only two that are slightly similar are the SEM and TEM, but even then they sill do different things. Furthermore, each microscope can be used for a variety of measurements (both qualitative and quantitative).
One interesting aside in the whole matter of microscopy is that at the nanoscale one must carefully consider how the sample could be adversely affected by different microscopy techniques.
This isn't such a big problem with a regular light microscope since photons have no mass. But when you're firing high-energy electrons at a target sample, damage is bound to occur. The lesson of the day is that in most cases, aside from the STM, using microscopy to visually represent your sample will also do some damage to it.
Another problem is that most microscopes require very stringent sample preparation. For the SEM, TEM, and STM, you need to have an ultra thin sample that is also electrically conductive. There are ways to get around this, but the fact remains that it could take hours to mount a sample correctly, not counting the hours that it might take the actually synthesize the sample.
In an interesting tidbit of trivia, both the SEM and TEM were the result of institutionalized research, while the STM and subsequent AFM were solely the work of Binnig and other researchers at IBM between 1981 and 1986.