So this morning one of our file server had a virus breakout which affected one of the shares on the server! All the files and folders under it were hidden and I could see copies of the existing folders under the root directory created as a folder type of "Application" and the size of each folder was 120 KB.
So that's how I figured out there was something wrong so we worked with McAfee and updated our .DAT files and after that the Anti-Virus was able to detect the trojan and delete it but I had to now un-hide all the folders using the attrib command and below is what I used..
C:\>Attrib -h -r -s /s /d d:\Public\*.*
Where Public was the parent folder which was affected and all the files and folders under it, after the command successfully finished the folder was now visible and no longer hidden!