In recent years, biomaterial investigators have increasingly focused their research on hydrogels and their capability to be fabricated into tissue engineering scaffolds. Although several fabrication methods have been used to produce hydrogel scaffolds, those methods are unable to routinely produce three-dimensional submicron and nanoscale scaffolds with precise control of the geometry, a crucial factor necessitated by the recent developments in the field of tissue engineering. Femtosecond laser-induced two-photon polymerization is a promising technique that fulfills these requirements. In our work, we used a femtosecond laser to fabricate three-dimensional submicron-scale scaffolds with poly(ethylene glycol) (PEG). The modulus, dimensions, and shape of the scaffold can be readily adjusted by changing both the laser parameters and the molecular weight of the PEG prepolymer. With the femtosecond laser, we also fabricated two-dimensional topographical patterns, which have important applications in basic biological research. To improve the throughput of femtosecond laser fabrication, we integrated the femtosecond direct-write process with a nano-imprint process by which the femtosecond laser is used to produce nano-patterned molds. We then carried out nanoimprinting to transfer the nanofeatures in the mold to the hydrogel in a massively parallel fashion.