If you are using Master File Table (MFT) for file copy and it has gone bad, you need to speak to your system administratior.
BTW, you have not told us what OS you have and if this is a desktop or a server. If you have serious hardware errors, some data may be permantly lost.
Otherwise, have you read this?
How to repair MFT - Windows XP SupportIf that is not help, and if the company administrator can not help you, come back here and provide some more details. There are some really sharp members hee that know the answer, they just need the details.