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How to locate Malicious or unwanted scripts in a Server 2008 R2 install?

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I am Managing two systems as part of a competition, Windows Server 2008 R2 and a Windows 7 Machine. The competition is the National Collegiate Cyber Defense Competition.

Part of my issue is i normally am very good at research but it's like i am unable to find this bit of info.

I need Answers to several issues.
1. Where can i locate Scripts at in Server 2008 R2?
2. Assuming scripts aren't in one specific directory... Is there a Freeware Tool i can use that can locate and identify what they do? Such as tot ell em if they are malicious or dangerous.
3. Is there a way i can block execution of any scripts in the system not created by a valid source?


Thank you very much for your assistance, regardless if my questions are answered it is nice if i can at least be proactive and actually ask instead of keeping silent. Perhaps future competitors will be helped by this so they don't have to spend months locating it.

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