How to make files accessible only by root?
Make sure that the owner of the application is root and set the permissions such that only the owner can run it.
sudo chown root:root /path/to/application
sudo chmod 700 /path/to/application
If you look now at permissions with ls -l /path/to/application, you should see the following: -rwx------ root root, meaning that root can read, write and execute, and anyone else cannot even read that file.
Change the permissions of this applications as a root :
chmod 700 application-name