all folders and exe files showing up as shortcuts

Could be caused by a virus that may have infected your system. Is your antivirus/antispyware all up to date?

In Windows Explorer when viewing the files, Click the View Menu and select "details".  Are the file "types" named "shortcut"?  Are the file sizes correct or are they the size of a shortcut (1kb)?

It's possibly caused by a malware. I've seen such a case many times!

If the malware is active on your PC you can't do anything to see your files, because it'll undo what you do!
If you don't have any malware and they're just effects of a previous inffection try this:

Open your flash drive window, then :
Start menu > Run > Type cmd and press enter > Type the command below

Attrib -s -r -h X:\*.*

(I assumed that your Flash drive letter is X. Change it to your flash drive letter (e.g. I))

Then press enter and wait for the command to finish and it goes to the next line.
Check your flash drive window for the files. If you see no files, then one of the 2 cases are possible:

1) The malware is still running on your system.
2) There is no file other than that shortcuts on that flash drive. (The real files got removed somehow)

Below is a link to a discussion of a similar problem. It is difficult to tell which malware affected you. Malwarebytes and Microsoft Security Essentials usually detected and remove such malware.

http://answers.microsoft.com/en-us/windows/forum/windows_7-files/files-on-external-drive-have-changed-to-shortcuts/695db4cc-645f-4bd1-85c7-41671457fe11