You wrote, "Now I can not find/open the folders though the files are there". The way I view it, finding a folder and opening a folder could incorporate two separate issues. Given the fact it's Win32/Dorkbot!lnk (found by MSE?), I'm going to presume you mean you're unable to find them, in order to open them.
As a start, I would try the easiest thing first. And that would be to "Unhide files and folders". Also remove the check mark next to " Hide protected operating system files". You haven't included which OS you're running. For: Windows XP / Windows 7.
Best of luck..
In my Seagate 500 GB External Hard disk recently, I noticed for the HDD, there are shortcut links for all the folders . I could open the folders in a new explorer window. Next day, antivirus detected attack in the HDD with Worm:Win32/Dorkbot!lnk. It deleted all the shortcuts. Now I can not find/open the folders though the files are there. I can understand the files are there during virus scanning or though disk usage.
Please help how to recover the data?