I have some sensitive data and I dont want to share with the root user. As fa as I know the root users can read and modify everything. My question is how can I protect this data. I don't want to give access to the root users to this folder/file.
In a Linux (or any Unix) system the root user has the ultimate power to do anything. There is no way to limit the root users ability to view, modify and execute any file or folder. This is more or less the point of the root user.
If you want to protect this folder/file the only thing I can suggest is encrypt it.
Ubuntu since 8.10 also offers to encrypt either the complete home directory of a user or a private folder. For more information see here