The deep state is made up of people in positions of power, and to destroy the deep state, you have to remove those people.

Trump cannot unilaterally fire a lot of civil service positions, but he can move those people around. He can have the military build a big Federal compound on Adak Island, Alaska, and transfer a whole bunch of deep state people there, and let them all sit at a desk staring at a wall for 8 hours a day, with resignation the only way off the island.