Simple. Don't put infected files on the external hard drive.
Sorry. Had to do it. If you're antivirus software is dated, update it or use a better antivirus program. Avast is a good free program. Scan the files you want to back up before backing them up. If those files are good, then you're probably good to go.
The tricky thing is if you download straight from the interwebs to your external. That's a riskier move. That's why I don't.

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