This study aims to establish and optimize a process for the fabrication of 3D microstructures of the biocompatible polymer Parylene C using hot embossing techniques. The different process parameters such as embossing temperature, embossing force, demolding temperature and speed, and the usage of a release agent were optimized, utilizing adhesive micropillars as a use case. To enhance compatibility with conventional semiconductor fabrication techniques, hot embossing of Parylene C was adapted from conventional stainless steel substrates to silicon chip platforms. Furthermore, this adaptation included an investigation of the effects of the hot embossing process on metal layers embedded in the Parylene C, ensuring compatibility with the ultra-thin Parylene printed circuit board (PCB) demonstrated previously. To evaluate the produced microstructures, a combination of characterization methods was employed, including light microscopy (LM) and scanning electron microscopy (SEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), and Fourier-transform infrared spectroscopy (FTIR). These methods provided comprehensive insights into the morphological, chemical, and structural properties of the embossed Parylene C. Considering the improved results compared to existing patterning techniques for Parylene C like plasma etching or laser ablation, the developed hot embossing approach yields a superior structural integrity, characterized by increased feature resolution and enhanced sidewall smoothness. These advancements render the method particularly suitable for diverse applications, including but not limited to, sensor optical components, adhesive interfaces for medical wearables, and microfluidic systems.