We report on the plasma etching of thick (~23µm) Parylene C structures. Parylene C is a transparent polymer that benefits from high biocompatibility, flexibility and chemical inertness, and has gained increased attention over the years in the biomedical field. In the manufacturing process, highly defined structuration steps of Parylene C are essential, but techniques based on laser, scalpel and wet etching have shown to be unsuitable for properly cut structures. Plasma etching remains nowadays the most widespread option, though fast etching rate, lack of residues and high aspect ratios are still hard to achieve. To overcome these issues, the selection of both mask material and plasma conditions is crucial. Here, three masks-metal, positive and negative photoresists-are tested as stencils, and several plasma parameters are briefly studied in order to obtain the highest etching rate while maintaining good coverage. We showed that increasing the RF power up to a considerable 2800W while maintaining a moderate physical contribution (bias power, pressure, temperature), is optimal in the achievement of fast PaC etching without inducing thermal stress. Besides, the addition of a short fluorinated plasma in the midst of the process is shown to alleviate residues. For the first time, negative photoresist Intervia Bump Plating (BPN) coating followed by ICP 1-RIE 2 are used in order to pattern Parylene C-based structures, with a clean cut, vertical profile and fast etching rate (~0.87±0.06 µm/min) and a selectivity of 0.5. This solution was carried out to release unitary Parylene-based neural probes from a silicon wafer. Finally, cytotoxicity assays on these neural implants were performed to make sure that no trace of mask or stripper residues would jeopardize device biocompatibility.