Massive malware infection has made a mess

I had a malware/trojan infection a few days ago that kept me occupied for the better part of two days with cleaning up using:

Malwarebytes Anti-Malware and Anti-Rootkit
AdwCleaner
Junkware Removal Tool
Norton Power Eraser
Sophos Virus Removal Tool
Trendmicro Housecall
SpyBot Search & Destroy
and Chrome Cleanup-Tool.

Now, when the smoke has cleared and I try to assess damage done, even the c:\users\MyName\appdata is gone(!) and I find files and and folders in completely new places, some empty, some not.

It is seemingly an unholy mess (but wholly a mess;) and I wonder if the best thing would not be to simply reinstall Windows 7 as it is next to impossible to distinguish what is whole and what is messed up.

Would a system restore really restore e.g. c:\users\MyName\appdata, a folder which is kinda, sorta useful?

So what say you? Would it be better beginning with a clean slate, or is there hope yet?

Clean install after running CLEAN ALL from DISKPART

Disk - Clean and Clean All with Diskpart Command

I presume, Göran, that you have not been regularly backing up your system with something like Macrium Reflect. May I urge you after following Golden's advice to install Macrium and make regular backups at least once a week. Then when you have a problem you can restore your system and be up and running again within the hour!

Golden said:

Clean install after running CLEAN ALL from DISKPART

Disk - Clean and Clean All with Diskpart Command

Thanks Golden. This would give me about as clean a slate as they come;)

"R U sure it's not just hidden? Some of those anti malware and virus apps will turn "view hidden files and folders" back to hidden in folder options so you may just not be able to see it."

Now you tell me;) Anyway, there's 106,304 files on the system drive to check, and at that point I had been awake for some 24 hrs straight not wanting to give up. At that point I gave up, and came here to write the OP.

After that I just went ahead and did what user Golden suggested and nuked the system drive - nuked it but good, then reinstalled Windows.

I could have never quite gotten rid of the nagging suspicion that, even if I had known about what you now tell me, there was still some bad code lurking in the depths of all those files, ready to pop up at some time in the future and wreak havoc anew.

I want my PC to be my PC, no compromise. Then I took that know-it-all whippersnapper Mitchell's advise and got Macrium and backed up the C drive on an external drive.

So I'm good. Thanks for replying though

Admiral Awesome said:

Then I took that know-it-all whippersnapper Mitchell's advise and got Macrium and backed up the C drive on an external drive.

Thanks for that - I haven't been called a "whippersnapper" since circa 1947