You should look at ESRF X-ray diffraction beamlines with microdiffraction capabilities (found this on the web: http://www.esrf.eu/UsersAndScience/Experiments/CRG/news/BM32-upgrade-microdiffaction).
There are some papers published where X-ray diffraction experiments have been performed with a resolution less than 300 nm. Not lower than 100 nm but close.
If you have access to an SEM instrument that can do EBSD, you can do Transmission EBSD. My friend is getting about 50nm resolution using this technique and is really cool. You need an electron transparent sample though. This is fairly new, but you can find some papers on this.
Yeah I guess if you have access to a nice TEM like that, you can do it. You can get a much better resolution with TEM (it is basically the same technique). It totally depends on what you have available.
You don't need STEM in SEM to do transmission EBSD. It is just a special setup and electron transparent sample. Here is an article that may help you understand the technique better.
http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2818.2011.03566.x/full
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