I managed to run default controller from sub directory by adding a MY_Router file in application/core, everything works fine but this is what I am facing now.I am unable to route it if url hits /admin or /student or /teacher which is eventually a sub directory in controllers.
https://s14.postimg.org/pr3ta38f5/controller_structure.png
https://s14.postimg.org/z05zk7hb5/error_1.png
https://s14.postimg.org/mmt5darmp/issue_2.png
https://s14.postimg.org/kwa4bta3l/page_controller.png
https://s14.postimg.org/j5voo2hy9/routes.png