What you are describing is brake pulsation. This occurs when the disc rotors become out of round. This condition is caused by the friction that builds up during braking which heats up the rotors and as they expand and contract the metal distorts and the end result is brake pulsation.
This is a common occurrence and with the proper equipment the rotors, provided they have the proper amount of metal remaining can be machined and balanced with a computerized lathe that machines and true’s them on the car. It is called the Pro-Cut. This device is required by most manufactures. The brake pads will be replaced at the same time thus restoring your brake system by to the original condition.
Joe