Pardon the relative ghettoness of my 5-second Photoshop work...but this should give you a rough visual idea of how it's done:
1.) The roof is cut across the car where the yellow marks are; sections of the a/b/c pillars are removed (green marks on picture), the larger the section the lower the top will be. The top will also usually have to be cut down the middle (from front to back) to account for the tapering of the side profile of the car.
2.) The frontmost cut section is moved forward and down, the middle section is moved down, and the rearmost cut section is moved back and down. Blue areas are openings left over. Doing this will prevent from having to redo all of the pillar profiles.
3.) Filler pieces are formed and welded in; same with the middle after it has been split. Result: chopped roof.