One of the limits of a conventional multiphoton microfabrication is its low throughput due to the sequential nature of scanning process. In this study, a multiphoton microfabrication system based on spatiotemporal focusing and patterned excitation has been developed to provide freeform polymer microstructures fast. The system integrates a 10 kHz repetition rate ultrafast amplifier featuring strong instantaneous peak power (maximum 400 μJ/pulse at 90 fs pulse width) with a digital micromirror device generating designed patterns at the focal plane. As the result, three-dimensional freeform polymer microstructures using Rose Bengal as the photoinitiator are created by sequentially stacking up two-dimensional (2D) structures layer-by-layer. The size of each 2D fabrication area can be larger than 100 × 100 μm2. Compared with scanning process or fixed mask pattern generation, this approach provides two-or three-fold fabrication speed and freeform microstructures. Furthermore, the system is capable of optical sectioning the fabricated microstructures for providing 3D inspection.