The self-assembly of block copolymer (BCP) thin films is a versatile method for producing periodic nanoscale patterns with a variety of shapes. The key to attaining a desired pattern or structure is the annealing step undertaken to facilitate the reorganization of nanoscale phase-segregated domains of the BCP on a surface. Annealing BCPs on silicon substrates using a microwave oven has been shown to be very fast (seconds to minutes), both with and without contributions from solvent vapor. The mechanism of the microwave annealing process remains, however, unclear. This work endeavors to uncover the key steps that take place during microwave annealing, which enable the self-assembly process to proceed. Through the use of in situ temperature monitoring with a fiber optic temperature probe in direct contact with the sample, we have demonstrated that the silicon substrate on which the BCP film is cast is the dominant source of heating if the doping of the silicon wafer is sufficiently low. Surface temperatures as high as 240 °C are reached in under 1 min for lightly doped, high resistivity silicon wafers (n- or p-type). The influence of doping, sample size, and BCP composition was analyzed to rule out other possible mechanisms. In situ temperature monitoring of various polymer samples (PS, P2VP, PMMA, and the BCPs used here) showed that the polymers do not heat to any significant extent on their own with microwave irradiation of this frequency (2.45 GHz) and power (∼600 W). It was demonstrated that BCP annealing can be effectively carried out in 60 s on non-microwave-responsive substrates, such as highly doped silicon, indium tin oxide (ITO)-coated glass, glass, and Kapton, by placing a piece of high resistivity silicon wafer in contact with the sample-in this configuration, the silicon wafer is termed the heating element. Annealing and self-assembly of polystyrene-block-poly(2-vinylpyridine) (PS-b-P2VP) and polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) BCPs into horizontal cylinder structures were shown to take place in under 1 min, using a silicon wafer heating element, in a household microwave oven. Defect densities were calculated and were shown to decrease with higher maximum obtained temperatures. Conflicting results in the literature regarding BCP annealing with microwave are explained in light of the results obtained in this study.