Large-scale network recording technology is critical in linking neural activity to behavior. Stable, long-term recordings collected from behaving animals are the foundation for understanding neural dynamics and the plasticity of neural circuits. Penetrating microelectrode arrays (MEAs) can obtain high-resolution neural activity from different brain regions. However, ensuring the longevity of implantable devices and the consistency of neural signals over time remains one big challenge. A potential solution is to use flexible, polymer-based MEAs to minimize the foreign body response and prolong the lifetime of neural interfacing devices. Rodents and nonhuman primates (NHP) are commonly used animal models in neuroscience and neuroengineering studies. Specially designed MEAs that capture morphological features of different animal brains and various brain structures are powerful tools to simultaneously obtain neural activities from multiple brain regions. In this work, we develop a set of prototype designs of polymer MEAs that cover cortical, sub-cortical, and multiple brain regions of rodents and NHP.