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I made a malware and virus scan in my system. As part of improving its performance. I restart the system but then it won't boot, so I tried loading the last known good configuration. Will it restore all the malware that has been removed by the anti malware I used?

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Generally the answer is no. The last known good configuration reloads only the CurrentControlSet in use the last time windows started completely. This normally is hardware drivers. As Moshe says the only exception would be a rootkit (generally). See http://support.microsoft.com/kb/307852 for a explanation.

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One thing to condsider is the System Restore. Make sure it is turned off and scan the system again. That is where many malware folks place code so that it reinstalls after a reboot. While Last Know Good will have little/no impact on the malware situation, the malware may return.

As mentioned, rootkits would also be an issue.

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I don't think so, unless the malware attacked your Windows system files - in that case it's probably a "rootkit". You may need a system restore or a complete reinstall.

What version of Windows are you running?

Vista and 7 have robust startup repair tools that can help you with this kind of problem.

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