An ion beam apparatus may include a chamber assembly configured to hold a material and direct an ion beam on the material, a detector configured to detect a signal generated from the material based on the ion beam being directed on the material, and a controller configured to control at least one parameter associated with the chamber assembly based on the signal, such that at least one of an ion energy associated with the ion beam, an ion current associated with the ion beam, and an incident angle of the ion beam with respect to a top surface of the material is changed continuously with time.