Most of your files are probably fine, anything you were accessing at that time may have become corrupted. Please say "PC" or "Mac" and I can help you further.
Here is where I asked the same question:
https://discussions.apple.com/thread/3949273?start=0&tstart=0
You need to download "Disk Warrior". It costs a lot of money, but if you know anything about downloading torrents with keygens or key codes you can get it for free.
Steps:
Download and install Disk Warrior.
Click "Rebuild" on the drive.
Preview the drive (this is where I drag and dropped the entire thing to back it up)
After it's backed up reformat and return the files to the flash-drive
What this is doing, is copying everything on the flash-drive to a new location. Since it is just a flash-drive, you should be able to fit everything onto your internal HDD. After this, you need to reformat your flash drive by going into "Disk Utility" and reformatting. Please remember that this erases EVERYTHING, so only do this AFTER you extract the files. If your flash-drive is bigger than 4GB and you use it on Macs, make sure to use MacOS Journaled. If you don't, you will not be able to transfer any files larger than 4GB using a Mac. If it is 4GB or smaller, you can use the standard FAT32 which is windows based. After reformatting your flash-drive, simply drag the files back onto the fresh and empty flash drive.
This information is catered to Mac users. If you have a PC, you can easily google Disk Warrior for PC or find it's equivalent. On a PC your Disk Utility may be called something else, but it does the same thing. Obviously if you only use a PC, formatting to FAT32 is what you want to do AFTER you extract the files.