We demonstrate the use of high-speed, multiphoton absorption polymerization (MAP) for the fabrication of large-area microfluidic master structures. High-speed fabrication in SU8 without laser-induced damage is made possible by the use of a novel photoacid generator with a high two-photon-absorption cross-section. Master structures fabricated with MAP can be used to produce polydimethylsiloxane microchannels with high aspect ratios and/or arbitrary cross-sections. Microchannels with different cross-sections and heights can be combined readily in a single device. This fabrication technique significantly increases the diversity of channel architectures available for microfluidic devices.