If you suspect the FAT boot sector is corrupt, you can check several of the fields listed here to see whether the values listed there make sense. For example, BytesPerSector will be 512 in the vast majority of cases. You would also expect to see text strings in the executable code section of the boot sector that are appropriate for the operating system that formatted the disk.
Typical text strings on FAT volumes formatted by MS-DOS include: “Invalid system disk.”; “Disk I/O error.”; “Replace the disk, and then press any key”; “Non-System disk or disk error”; “Replace and press any key when ready.”; and “Disk Boot failure.” Text strings on FAT volumes formatted by Windows NT include: “BOOT: Couldn’t find NTLDR.”; “I/O error reading disk.”; and “Please insert another disk.” You should not regard this list as being all-inclusive. If you find other messages in the boot sector, this does not necessarily indicate that there is a problem with the boot sector. Different versions of MS-DOS and Windows NT will sometimes have slightly different message strings in their boot sectors. On the other hand, if you find no text whatsoever, or if the text is clearly not related to MS-DOS or Windows NT, you should consider the possibility that your boot sector may have been infected by a virus or that some other form of data corruption may have taken place.
To recover from a boot sector that has been infected by a virus, it is usually best to use a commercial anti-virus program. Many viruses will do much more than just write data to the boot sector, so manual repair of the boot sector is not recommended, as it may not completely eliminate the virus and in some cases, may do more harm than good.
If you suspect that the boot sector was damaged for some other reason, it is usually best to use commercial disk recovery tools. While it may be possible to recover from boot sector damage without resorting to reformatting the drive by manually modifying the fields described above, manual editing of boot sectors should only be attempted as a last resort and cannot be guaranteed to work in situations where other disk structures may also have been damaged.
By Microsoft Support