Creating the Directory Structure
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Once you have created a TrueCrypt Volume, you need to create the necessary Folder structure on the encrypted partition.  There are several ways to handle this.

      If you are planning on installing one of the suites of applications available from PortableApps.com, you can simply install this into the encrypted volume- this will create the needed structure.
       You could simply copy the contents of your "Documents" directory from your USB host to the Encrypted drive and create a "PortableApps" folder in the root of the encrypted drive
      Or you could manually create the following directory structure:
      \
      + \PortableApps
      +\Documents
                  +\Downloads
                  +\Music
                  +\Pictures
                  +\Video