I don't think I would trust a flash drive yet. I don't know how reliable they are for long-term storage.
Drag the tracks you want from iTunes to the flash drive open in a Finder window. You may need to do this album by album and put them in folders structured as you desire. When you see them in iTunes they are organized using data stored in the file and not organized by folders as such.
Alternatively, use the File > Reveal in Finder command to show where the actual media file is located in a Finder window. Go up one level and copy the folder containing that album to the flash drive.
What are the iTunes library files? - http://support.apple.com/kb/HT1660
More on iTunes library files and what they do - http://en.wikipedia.org/wiki/ITunes#Media_management
What are all those iTunes files? - http://www.macworld.com/article/139974/2009/04/itunes_files.html