Three-dimensional biomimetic scaffolds have widespread applications in biomedical tissue engineering because of their nanoscaled architecture, eg, nanofibers and nanopores, similar to the native extracellular matrix. In the conventional "top-down" approach, cells are seeded onto a biocompatible and biodegradable scaffold, in which cells are expected to populate in the scaffold and create their own extracellular matrix. The top-down approach based on these scaffolds has successfully engineered thin tissues, including skin, bladder, and cartilage in vitro. However, it is still a challenge to fabricate complex and functional tissues (eg, liver and kidney) due to the lack of vascularization systems and limited diffusion properties of these large biomimetic scaffolds. The emerging "bottom-up" method may hold great potential to address these challenges, and focuses on fabricating microscale tissue building blocks with a specific microarchitecture and assembling these units to engineer larger tissue constructs from the bottom up. In this review, state-of-the-art methods for fabrication of three-dimensional biomimetic scaffolds are presented, and their advantages and drawbacks are discussed. The bottom-up methods used to assemble microscale building blocks (eg, microscale hydrogels) for tissue engineering are also reviewed. Finally, perspectives on future development of the bottom-up approach for tissue engineering are addressed.