Leroux: Unfortunately it's only my netbook and it doesn't have a cd drive. :(
I could download and copy stuff to my USB stick though.

JMich: I recall a certain malware that would make all folders hidden and then create a copy of itself with the folder's name, which when clicked would open the folder. Did you try checking if this is the case with the folders? Since it is quite possible that this (or another) malware will prevent you from toggling the "Show Hidden Files and Folders", open a command prompt, go to the directory your folders should be in (for example, c:\users\leroux\documents) and do a "dir /ah" which should show you all hidden files and folders.
Btw, what is the error message when you try to update malwarebytes?

AlKim: Something very similar happened to my girlfriend's netbook, although the details are vague since I wasn't using the computer when it occurred. Anyway, it turned out that almost all folders and files were hidden, but they existed nonetheless, so we made everything visible again and backed up all important files. The netbook was useless to all intents and purposes, and I couldn't fix it with System Restore, MalwareBytes or MSE. I couldn't revert to factory settings either because apparently that part of Windows was missing for one reason or another. Two days later the computer refused to boot up (it would start, but it restarted before it got to Windows), and I couldn't fix it by reinstalling Windows from a USB stick because the damn thing didn't even know it had a hard drive installed. So I changed the hard drive to a fresh one, but got the exact same result. At that point I ran out of ideas.

Better make backups of your files in case it turns out you've got the same problem she had.

xyem: RAID is by no means a backup. It's simply there to reduce the inconvenience of a drive failing (to nearly zero) :) It's quite possible for the other drive to fail while it is rebuilding - at which point, my actual backups would be mobilised to remedy the situation!
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Depends how you look at it. At the most basic, all disks are brought for the same purpose (storing data). The purpose of buying a second disk is to allow redundancy, which the first can't do alone.

Whether it is worth it or not (on any budget) depends on how valuable it is to *you* that your machine stay working following disk failure. As nearly everything I do revolves around my computers, it is very worth it to me! Though I admit, it was technically free, as the RAIDed drives in my desktop were spare from my server storage upgrade :)
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The problem may not be a mechanical failure, but a software one, making writing anything to the drive, even a "small delete" really dangerous. If the file information is corrupted, that "small file" may be pointing at random parts of a whole bunch of other files where deleting it would corrupt those too. The chances of it being this sort of corruption is considerable due to the symptoms (random directories being inaccessible).

The very first step in any possible drive related issue is to stop anything writing to the drive!

Leroux: Hm, too late. I already connected the external to the PC in safe mode, hoping to save my data. :(

Can a virus damage it just by connecting? And does this sound like a virus rather a malware attack? Would copying infect the other hard disk, too?

DukeNukemForever: It's possible but maybe not very likely. From your description I would guess there is a high possibility you got malware, but that's not relevant at the moment. First step should be to make a backup without booting from your infected system or defected hd, in both cases you need to boot from cd or an usb-stick. It's very likely that in the case of a virus your some of your files are infected too, so after a backup you need to scan your files too.

Leroux: Ok, I'll just hope then that the external was not infected yet, download a Knoppix CD and go over to a friend to burn it now or tomorrow. I've never worked with Linux before though. I hope it's user friendly enough for a long time Windows user to grasp the basics? And in case the booting with Linux does not change anything about the hidden status of the files, how would I go about copying them?

DukeNukemForever: I didn't use Knoppix for a while and so would prefer Ubuntu. Regarding hidden files this is maybe helpful for you: http://www.howtogeek.com/howto/ubuntu/view-hidden-files-and-folders-in-ubuntu-file-browser/

DukeNukemForever: If you really got a virus I highly recommend not to connect your external hd or anything else with sensitive data to your infected system. Be patient, get your disc to boot from cd and then copy all your data. It's the safest way against data loss.

Though if you really want to go the other way, get a portable file manager and copy it to your usb-stick. As example, you can install Total Commander on your netbook and make a portable version for your usb-stick: http://www.ghisler.com/dusbinst.htm

Edit: If you do that, be aware of that there is also a risk to infect your netbook through the usb-stick. So really, do a backup of all your important data on your external hd through a clean system (booted from disc or usb-stick) and then try to repair or clean your system.

GameRager: If it's a copy of your data then how is it not a backup(technically speaking), or at the very least the makings of one if need be?

GameRager: I use mine to store additional data, thus allowing me to have more on the same system. I only make backups of important data, not every single thing on the system.

GameRager: Still, if it is malware related and the MWB has become infected this is the best course of action. Ultimately it's up to him to decide.

Leroux: Thanks for the link! So I take it Ubuntu is easier to use for a Windows user? I'm going to try that then. I'll get back to work now and give you all a rest. I'll probably report back tomorrow. ;)

Thanks everyone for being such an awesome and helpful community!

GameRager: You could always scan the USB stick when you pop it into the other/clean PC before running anything on it, and sandbox it as well.

lugum: why throw away money to let someone do stuff what you can do yourself?

first check for malware and stuff. http://www.malwarebytes.org/

xyem: It's a backup in case of physical drive failure, it is not a backup for the many other things that cause data loss. Everything the originals are subject to, the "RAID copy" is subject to as well. Accidental deletions? Copied instantly. Malware introduced? Copied instantly. Malevolent intrusion? Copied instantly. Even the drive containing the originals failing can cause the drive failure of the copy, as the second disk can fail under the strain of rebuilding (which is one reason why you are not supposed to use similar disks).
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RAID0 would also allow you to have more on the same system (and make read operations faster too) but the failure of either drive would render all data inaccessible. Fun fun!

I have RAID1 on my three main machines (2 desktops and server) only to stop a drive failure taking the machine offline. My backups are similar to yours as they are not full disk images, but do contain everything important.
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The problem being that he doesn't know if it is malware related and every write to the disk could be causing him to lose more and more data. When your data is at risk, you always go from the most conservative options first..

DukeNukemForever: He should do that in any case now, but it's unnecessary to run an infected system and attach other writable devices to it. There is always a risk that the virus scanner can't find the virus.