I have millions of audio files, generated based on GUId (http://en.wikipedia.org/wiki/Globally_Unique_Identifier). How can I store these files in the file-syste
That's very easy - build a folder tree based on GUID values parts.
For example, make 256 folders each named after the first byte and only store there files that have a GUID starting with this byte. If that's still too many files in one folder - do the same in each folder for the second byte of the GUID. Add more levels if needed. Search for a file will be very fast.
By selecting the number of bytes you use for each level you can effectively choose the tree structure for your scenario.