I want to verify if file/folder exists on my CI system (not system folder), can i do it from controller or I need create a method on my model to do it?
It's basically a matter of choice. You can define your function in both your model and controller. But if you want to use it over and over from different controllers, then better define a new model and put that function in it. I'd define model which is to be used by many controllers that is having some common-general methods. Just to keep things apart and maintaining them later. Helpers are also a way to keep things separate.