The fabrication of high aspect ratio (5 and above) microstructures based upon UV embossing of mixtures containing poly(ethylene glycol) diacrylate (PEGDA) is described. UV embossing is a quick and convenient replication technique using low pressure and room temperature. The biocompatibility and cell- and protein-resistance of PEGDA make deep three-dimensional (3-D) micropatterned PEGDA films potentially useful for many biological applications such as protein delivery, tissue engineering, drug delivery, and biosensors. Microarrays of deep microchannels and microcups separated by PEGDA walls with aspect ratios of 7 and 5, respectively, were successfully embossed. UV embossing was found to faithfully replicate the lateral periodicity and height of the mold. We also successfully UV embossed a mixture having equal weight proportions of hydrophilic PEGDA and hydrophobic poly(propylene glycol) diacrylate and demonstrated the use of this microarray of microcups for encapsulation of a model protein (bovine serum albumin) within a UV cured PEGDA hydrogel; a protein encapsulated within a hydrogel 3-D microarray was fabricated. Although high aspect ratio UV embossing has many attractive features, it is a difficult process to implement, requiring precise control and optimization of mold, process, and material parameters. Successful high aspect ratio UV embossing was achieved using two molds: a rigid nickel mold and a silicone rubber mold. The latter did not require any surface treatment, but the nickel mold was found to require coating with a cured silicone resin to obtain a suitable nonstick surface. The UV exposure time was controlled to optimize the hardened resin strength while avoiding excessive brittleness. Peel-off of the hardened microstructures was performed at a small angle to avoid breakage of the molded structures. A mold release additive was necessary for successful demolding. Trimethylolpropane triacrylate, a high shrinkage monomer, also facilitated demolding.