If you are just backing up files then clean everything as much as you can. Backup and then before you restore install the latest version of your AV and update it. restore to a directory, scan it with your current AV and then scan it again with another AV online (Trend etc). You can never be 100% sure it is clean though.
Security changes all the time and the field is massive so you will need to narrow down your request a bit more.
Keep your operating system up to date. Use a good firewall, antivirus and antimalware. Keep definitions etc up to date. Use common sense regarding the websites you visit, the content you download, the software install and the ports you open in your firewall.
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