route dose not work to sub folders

Yes, don't alter anything in /system. It's completely unnecessary and will make upgrading a pain since you basically replace everything in /system, so you'd have to reimplement all of your custom changes each time you upgrade. You can extend the core and add new functionality, or override existing functions with your own.

See the docs for "extending core classes": http://www.codeigniter.com/user_guide/ge...core-class