I am designing an online back up system for my school project, I know there are plenty of applications that can be used to upload and download files to and from a server, the problem is I don't seem to have a guarantee of security for the files. Any opinions will be highly appreciated!

What kind of security are you asking about?

If it is encrypted traffic, you can use EFTP, VPN, and possibly others as well.
If it is about ensuring that the file have arrived safely, you might be looking for something like robocopy.

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