Microwave annealing enables rapid (60 s) ordering and orientation of block copolymer films. The developed morphology in polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) thin films depends on details of the heating rate that is controlled by microwave output energy as well as the sample location in the microwave. Over a wide heating rate (1.1-2.7 degrees C/s), perpendicular orientation of the cylindrical mesostructure at the surface is >50% after 60 s, but goes through a maximum at 1.8 8 degrees C/s leading to approximately 97% perpendicular cylinders at the surface. The propagation of this perpendicular surface morphology through the film thickness is also dependent upon the microwave annealing conditions. The surface structure evolves with the microwave annealing time from imperfect ordering to perpendicular cylinders to parallel cylinders as the annealing time increases. This work demonstrates the importance of controlling the heating rate during microwave annealing, which will be critical for optimizing microwave conditions for directed self-assembly. (C) 2016 Wiley Periodicals, Inc.