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Macbook pro OS X 10.9 If I backup using time machine and 3 months later decide to restore it back because I have a virus, would it be able to eliminate the virus? Also does time machine delete all the new files i've added since then?

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If you believe your Mac has a virus or any kind of malware you should clean your Mac using a piece of software designed to remove malware. Time Machine isn't intended to be used to remove malware. There is nothing to stop a piece of malware from infecting your Time Machine backups.

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