Ensure that the latest drivers are installed.
Run Chkdsk <driveletter> /f
This is a destructive rewrite of indexes and attributes of files. So do not run this unless you have a good backup.
If possible, It will Fixes errors on the volume and make the drive NTFS again.
Once verified (through diskpart) that the drives are in ntfs format run bootrec /rebuildbcd
Verify that it finds and indexes the os volume
Attempt to boot the server
If still does not boot, restore from backup.
You will need to find out why your hard drives ended up going to RAW format. Whether it was hardware failure, os corruption, virus, etc.
Pull Event logs
Location: Should be in C:\Windows\System32\config or C:\Windows\System32\winevt\Logs depending on OS
View Windows Prefetch
This records what on the system is accessed. Mark McKinnon created a tool created for parsing this data.
Registry is stored in C:\Windows\System32\config once backed up you can view the following info
View Last logged on user
View Last key edited by RegEdit
You can try and Run the following 3 commands from the 2012 recovery DVD under Repair your computer, however it can not fix the mbr or even see the bcd while the disks are in RAW format