Step 1: Read my tutorial for creating folders. The same warnings apply. There will be two versions to this. One which is easy and is low risk but gives less sorting abilities. The second involves the techniques from my first tutorial so it would be wise to bone up on that one before you try the harder version of this tutorial.
The Easy Way:
Step 2: There is a difference between a software switch and a hardware switch on the Cr-48. You will need to enable the software switch under "About Chrome Os" and my clicking "more info" and changing beta to developer. (You may not need to do this; if you can do the next step then you can skip this step)
Step 3: In the omnibox type "about:flags" this will give you options that are still being developed and might not work.
Step 4: Enable "Advanced File System" and anything you want to try or find useful. I recommend the Media Player and the web page pre-rendering.
Step 5: Hit the "Restart Button at the bottom of the page.
Now comes the fun part.
Step 6: Plug-in your flashdrive.
Step 7: There should be a popup with your files and data, if not then you should be able to access it later by hitting "ctrl + o" (that’s an oh not zero) and then hitting back on the popup so you can find your flashdrive.
(Just realized that you can just right click the names of your files in this popup and just "Save as.." them to download them to the computer but there are good things to know in the rest of this tutorial even if it's harder. I promise"
Step 8: Find a .txt or .pdf or .mp3 or any file that is supported by Chrome OS and open it.
Step 9: In the Omnibox there should now be a "url" of sorts for where your file is. Remove from that url the name of your file but leave the name of the folder it is in.
Step 10: If you don't see the names of your files in the Chrome window instead of the popup then you didn't do it correctly (or I explained it poorly)
Step 11: You can now use this directory to find your files and folders in directory format and you can "right click" on them (or "alt + click mousepad") to save them.
The Hard Way (involves the command line)
Step 1:This is where reading the Folder tutorial is key. (cause I don't want to retype it) Open the command line.
Step 2: Plug in your flashdrive
Step 3: Find your flashdrive in the command line. You can do this by typing "cd .." two or three times in a row. This will take you to where your "media" folder is.
Step 4: Type "cd media" and then type "ls" in order for you to determine the name of your flashdrive.
Step 5: Type "cd nameofyourflashdrive" You should now have access to it and the files which you can view by typing "ls"
Step 6: To move this to your Downloads folder your going to have to remember where it was. It should be in the home/chronos/user/Downloads directory. And your flashdrive should have the directory of media/nameofflashdrive/file.
(Remember, that moving it is the same as "cutting" it. I will show you how to "copy" next.)
Step 8: Type "mv media/nameofflashdrive/file home/chronos/user/Downloads" or if you are in the folder that has the file you can just type the name of the file instead of it's directory.
Step 9: To copy "dd if=/media/nameofflashdrive/file of=/home/chronos/user/Downloads/file"
Make sure you "create" the file in the "of" command otherwise it will not work.
That should be everything. If there are questions I will gladly advise.
EDIT: It's been about two years since I made this post and it may not be entirely accurate and up to date as I would like since I bricked my CR-48 soon after. I'm pretty sure they added file management sometime afterward but this post somehow has stayed popular and relevant so I'm not sure. I would appreciate any feedback and I will edit this post as need be.