boot in administrator mode
run
sfc /scannow (system file checker verifies integrity of the entire windows operating system using crc hashes and replaces any files modified by virus or trojan with the original including even DLL files...)
Some of the files might not have been replaced, to see which ones we need to sort
them out of the log and put them into a new file so we dont have to read a book to
find the right ones.
Right click command prompt in the start menu under accessories and click 'run as administrator' then if it asks for the admin password - give it to it.
Then type in this command to sort out the string to a new file.
findstr /C:"[SR] Cannot repair member file" %windir%\logs\cbs\cbs.log > c:\stuff.txt
that just put everything into a file called stuff.txt in the root of the c drive.
We have to fix these manually.
in your elevated command prompt just type:
notepad.exe c:\stuff.txt
this will open notepad in windows with the list of the ones that sfc could not fix, which of course is the list of the ones we have to fix manually.
Let's say one of those files is named blackbox.dll (which is in every windows)
To replace it type this in your elevated prompt.
EDIT : USE CACLS IN WINDOWS XP NOT ICACLS...
takeown /f c:\windows\sytem32\blackbox.dll
icacls c:\windows\system32\blackbox.dll /grant Administrators:F
copy d:\temp\mywindowsgoodfiles\blackbox.dll c:\windows\system32\blackbox.dll
Do that with each one that windows could not replace in the list we made in the file and when you are done you have a 100% windows machine.
This procedure works on xp, vista, and windows 7.
Once you are done reboot the pc so that you are running a 100% verified authentic windows o/s and not one where any system files are infected by viruses or trojans.
i suggest you also run
sigverif - it's used to verify the digitally signed critical files.
EDIT: sigverif and sfc are part of windows xp, vista, and 7.
*** it may also help you to run these: dial-a-fix, lspfix, and hijack this, along with a scanner like avast (which can do a preboot scan) and some antitrojan ware like malware bytes, spybot, or lavasoft's adaware.
**** If you use sfc /scannow or the boot option it will ask for your windows installation cd to get KNOWN good files from.