While the Confederacy did not mount a full-scale invasion of the Commonwealth after the fall of 1862 (the Heartland or Perryville Campaign), they did have a successful guerrilla campaign throughout the region. Hiding back in the "sticks", these rebels would pop out, hit a target, and disappear back into the hollows before any pursuit could be summoned. Louisville was the Union Army's primary supply depot and new recruit training facility for the Western Theater, yet a number of Confederates managed to hide less than thirty miles away in a large hollow just two miles from the L&N railroad, the Union's main supply artery to the forces campaigning in Tennessee and points south. Today that hollow is known as Guerrilla Hollow; it is located in the Bernheim Forest Nature Preserve and boasts a popular hiking trail.
How many Tanks, or aircraft did they have?
All they have to do now is turn of the electric and close the roads and rivers, those that can't survive on their own will give up.
It all depends on how brutal the government is willing to get. Waco was likely a test case.