Poly(dimethylsiloxane) (PDMS) is a widely used polymer in biomedical and microfluidics research due to its optical transparency, castability, gas permeability, and relative biocompatibility. However, while the favorable intrinsic properties of the polymer are typically suitable for preventing experimental artifacts, the true advantage of these devices often comes from their customized patterning and design, which can be tailored to specific applications. Critical parameters in biomedical applications such as chemical concentration profiles, fluid streamlines, substrate topography, and mechanical stiffness can all be fine-tuned simply by selecting the appropriate dimensions and arrangement of PDMS microstructures. To address challenges in expanding the application of PDMS-based devices to include handling more complex bodily fluids (e.g., blood, milk, etc.) and sensitive cell types (e.g., embryos, stem cells, etc.), customized design and surface engineering protocols must be developed. In the work performed in this thesis, we first use customized PDMS embryo culture wells to demonstrate hydrophobic small molecule absorption on native PDMS substrates despite the presence of bovine serum albumin and the arrest of early mouse embryos on osmolality-controlled PDMS substrates. We show that the effect is simply mitigated by adding a Pluronic F127 coating prior to culture, which significantly blocks small molecule sequestration on PDMS substrates. Next, we use a rotating shaft to apply tunable shear stresses in PDMS embryo culture wells to decouple the independent effects of shear stress on preimplantation mouse embryos. We then developed a PDMS microfluidic device to facilitate at-home nucleic acid collection on FTA Elute Micro Cards. Finally, we leverage PDMS-based micropillar arrays to measure the contractile forces of individual epithelial and fibroblast cells to assess the changes in myosin-based contractility in response to lead treatment. Together, this thesis work expands the applications of PDMS-based devices to serve as a substrate for sensitive cell types and process body fluids with complex compositions by proper surface engineering and design. The newly designed devices have the potential to significantly improve women’s health by augmenting embryo culture efficacy for in vitro fertilization (IVF), expediting breast cancer diagnoses, and adding depth to our understanding of the impact of small concentrations of lead.