Corruption in D:\$MFT. How may this progress? I don't think CHECKDB is useful here?
Here is how I would approach that issue.

Take care of SQL Databases.


Full backup of databases
Restore databases to development/test server
Run CHECKDB on development/test server on restored databases to check for errors.


If errors are encountered when running CHECKDB then you should address those issues, it means corruption happened somewhere in the line.  Seperate topic for recovering for this. 

Take care of drive on server


stop SQL Server process.
run CHECKDSK /r on drive
Hope for best.  There are stress test utilities out there that can tell you if the drive is having problems.  If this is a single drive, then consider replacing it.  If part of a raid group, find a health check utility from the manufacturer and see if that tells you anything.


If CHECKDSK /r fixed the issue with the Master File Table then you should run CHECKDB on the databases again to make sure there isn't any corruption (or any corruption introduced into the files by CHECKDSK /r.  

Side Notes:


Do you have PAGE VERIFY by CHECKSUM set for each of the databases?
When you do backups, do you use the CHECKSUM option?