Microphase separation of block copolymer (BCPs) thin films has high potential as a surface patterning technique. However, the process times (during thermal or solvent anneal) can be inordinately long and for it to be introduced into manufacturing there is a need to reduce these times from hours to minutes. We report here BCP self-assembly on two different systems, polystyrene-b-polymethylmethacrylate (PS-b-PMMA) (lamellar- and cylinder- forming) and polystyrene-b-polydimethylsiloxane (PS-b-PDMS) (cylinder- forming) by microwave irradiation to achieve ordering in short times. Unlike previous reports of microwave assisted microphase segregation, the microwave annealing method reported here was undertaken without addition of solvents. Factors such as the anneal time and temperature, BCP film thickness, substrate surface type, etc. were investigated for their effect of the ordering behavior. The microwave technique was found to be compatible with graphoepitaxy and in the case of the PS-b-PDMS system long range translational alignment of the BCP domains was observed within the topographic patterns. In order to demonstrate the usefulness of the method, the BCP nanopatterns were turned into an ‘on-chip’ resist by an initial plasma etch and these were used to transfer the pattern into the substrate.