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I am trying to setup my own linux ftp/apache/ssh web server. The server is going have 2 drives. One for OS and one for backups.

How can I deny any remote access to backup drive (even for admin if possible), except if user is connected to local network or is sitting physically in front of the computer?

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You cannot deny access to the root user. On the other hand you should not allow remote access for the root user anyway.

Once you made sure that onyl the root-user has access (chmod 700 on the mountpoint of the backup drive) part of your question would be answered.

If you still want someone else to have access to the data it is going to be more difficult and you'll have to look into unix-groups see here and Apache access control

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