How can I repair FAT32 and NTFS HD boot sectors?

By jgvera
Feb 17, 2005
  1. Hi! Please help me!

    Whole story (not really needed, find specific questions below)

    One day my WinXP didn't boot, there were missing files and it asked me to use the instalation CD to load the recovery console or something. But the CD didn't detect the hard drive, a message "Press F6 to install SCSI or... " was displayed for a few seconds and then nothing, no further response from the system. Tried many times restarting the PC but with no different result.

    Having Norton Antivirus always updated and being always very careful with all those matters, I never imagined that my problem was a virus. The hard disk was very old and I thought that was a good reason for the boot sector to fail.

    So I installed a new hard disk as master and the old one as slave. The installation CD detected the new hard disk and ran properly. I made two partitions, I installed WinXP in the first and copied my files (from the old hard disk) to the second partition. I checked both disks with Norton Antivirus and ScanDisk and found nothing wrong.

    I wanted to use the old hard disk to backup my files every day, so I made it FAT32 to be able to access it while booting from a Win98-made MS-DOS disk, in case of disaster.

    Everything worked great for a week, but then the new hard disk had the same problem that the old one had at first. WinXP doesn't boot. The installation CD doesn't detect any of the hard disks. Just the same, so it has to be a virus right?

    I can access the contents of the old hard disk booting from the MS-DOS disk. But I cannot access the contents of the new hard disk because its NTFS.

    Using very old Norton Utilities I can see the sector 0 of the old hard disk and there's something written on it: "Invalid boot sector". The new hard disk probably has the same problem.


    1) How can I repair a FAT32 HD boot sector? I wouldn't mind to format it and lost what I have there. That's already backed up. But my MS-DOS disk has no tools at all.

    2) How can I repair a NTFS HD boot sector? I would like to access, if possible, a couple of files I didn't have the chance to back up. I got an evaluation avast! BART (Bootable Antivirus and Recovery Tools) but doesn't detect the NTFS HD nor the FAT32 HD and the system stop responding, just like with the Windows XP installation CD.

    3) After doing that, I'm sure I'll be able to install WinXP again. What's the best antivirus? Norton is not. McAfee? Avast? PC-Cillin?
  2. Samstoned

    Samstoned TechSpot Paladin Posts: 1,018

    it's better to LLF write 0's to the hard drive and start over
    virus's can block file clusters from being accessed by making them seem to be bad
    so a reg format just erases the file allocation tables
    this tell your hard drive to write to that space if needed
    fixing the boot sectors may not solve the problem
    I know have been down that road
    best av is kaspersky after that McAfee get the latest
    just my opinion
  3. jgvera

    jgvera TS Rookie Topic Starter

    Useful tool!

    For future reference, I was able to back up the files I wanted from the NTFS partition using the "NTFS Reader for DOS" (freeware) included in a DOS bootdisk. Look for that in Google, I really recommend it! The disk has other useful utilities, although only in demo versions.

    Thanks for the reply and information Samstoned!

    I have already done the "low level" format on the boot sector (which, I think, destroyed the virus), deleted the Master Boot Record, created new partitions and given them "complete format". However, everytime I LLF and restart the machine I found that the boot sector says "Invalid entry... Operating System missing..."

    I have already put data back on the disks. Both have their identities back (when the virus was active they changed their IDs everytime I restarted the pc, sometimes they "were" CD drives or different kind of HDs). Everything seems to work just great. The only problem remaining is that I can't make the disks bootable, although I have "done" it during the partition processes and I don't want to buy another HD. So, how can I restore the system files on the boot record? Is that the right question?

    While writing this, I found out that Seagate has a program that prepares the disks to install OSs. I'll try that.

    I'll get the McAfee. I used to have it in an old PC and remember it scans the machine during booting, which would have prevented me this trouble.

    Again, thanks for the reply!
  4. Samstoned

    Samstoned TechSpot Paladin Posts: 1,018

    I use the seagate programs for every new disc prep I do
    also great for copy system to new bootable disc
    did you say you reinstall the old system files ( like image)
    back on the drive MMMMMMM :monkey:
    and sure once you write O's to disc you have no MBR
    it'sa blank are the reinstalled files older than before you got the virus?
    realblackstuff wrote in another discussion about
    using the OS disc to repair the MBR I have never needed to use it :chef:
    do search here for mbr repair now maybe thats not the right question
    maybe what you want is the registry files that point to your other programs
    thats another beast.
    if you didn't back that up your done
  5. jgvera

    jgvera TS Rookie Topic Starter

    Yeah, I found Seagate's software very very useful, and their HDs very good, they survived all what I did to them during all this time!

    Well, I had the idea that the executable code on the MBR (what I wrongly called system files) was wrong or damaged. Now I know that code is created along with each new partition.

    Now, I'm not sure if it was virus. One month ago, my problem was that WinXP didn't boot. I received messages about a missing driver (pci.sys) and another that requested me to use the WinXP CD to repair the system. But when I tried that, the installation program was not able to detect my old HD and I had to "reset" the PC everytime I tried to run the program. I bought a new HD and after a couple of attempts the program did detect it and installed Windows on it.

    But WinXP worked for only a week and then the same messages were displayed and I had exactly the same problem with the installation program. But one week ago I was browsing the installation CD and find out that if the installation program had troubles detecting HW one should press F7 instead of F6 when that's requested, in order to load the Hardware Abstraction Layer skipping some steps.

    That way the installation advanced a little more and, when it stopped, it said that it was not possible to continue. But at least that time I got information to work on: "error code 4". I looked for that at the MS Knowledge Base and after a whole day I was able to find an article that described exactly my situation: "missing pci.sys", "use CD", etc. One of the possible causes of the problem was damaged HW. And the provided solution was to uninstall HDs and RAM cards one by one until find the damaged device. I hoped there were nothing damaged so I just put out and in everything. And that was it! The program ran and installed Windows.

    I guess it was a RAM card not properly "installed", because when I put in the new HD I put in and out all the drives' connectors and all of they worked fine. But, I had not opened the PC in years before my problem! Did the card get slightly out by itself? And why did the machine work for a week when I put the new HD? And why was so hard to find information about an error in the so called Knowledge Base?

    Well, I just got back to let people know about this.

    Thanks for the feedback Samstoned!
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