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Functional and Security Best Practices: File Upload in a public facing visualforce page

I have worked on providing users to upload multiple websites for internal facing website. 
But wondering what are the defined best practices in terms of functional and security best to enforce in terms of apex/visualforce layer in order to ensure malicious files are not uploaded via the public facing website built on the platform?
Any thoughts and shareable experience would be greatly appreciated :)

Correction in first line: I have worked on prodiving users to upload multple files for internal facing website.