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I have read that if your computer gets hacked you can't be really sure that you have a clean system even if you manage to stop the hacker and the best thing to do is to reinstall your OS. Do you agree with this?

What about different types of file including audio,video,pdf and executable files. If I move them to an external drive is it enough to scan them with an antivirus? If the antivirus says that it did not find any threats, can I trust it? Is it correct at least 99%?

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Sometimes scan with an antivirus is not enough. Antivirus software is good for preventing the viruses and other malware from getting into your system and from operating there, but once they are in, sometimes it is almost impossible to clean them out. More to say, there are a lot of types of adware that are not detectable by any kind of antivirus software. Moving your files to external drive won't help either, if you are doing it using your current OS. Definitely the best solution is to back-up all the files you need and do a CLEAN OS installation after formatting your HDD or SSD. You can also try using virtual machine or sandbox software, in case you often deal with dangerous files.