Hey there, rithwikmoro.
This is a pretty unfortunate situation indeed. You should never store important files on a flash drive or a memory card without having a backup copy somewhere else.
You could try the flash drive via a different computer, to see if the same thing happens. If that doesn't help, you could try accessing it via Ubuntu Live USB (this is a portable, freeware, bootable version of Linux), to see if it's properly recognized and if you can get to your files. If that doesn't prove useful as well, you could go for data recovery programs:
http://www.tomshardware.co.uk/forum/id-1644496/lost-data-recovery.html and http://pcsupport.about.com/od/filerecovery/tp/free-file-recovery-programs.htm.
If all else fails, your last option...