Here we report on the plasma etching of thick parylene C in order to define flexible implantable probes for neural applications. To reduce the foreign body response and to ensure a good stability for chronic in vivo recordings, the chosen substrate for the neural probes is Parylene C, a polymer known for its high biocompatibility, flexibility and chemical inertness. In the manufacturing process, highly defined structuration steps of Parylene C are essential. Techniques based on laser, scalpel and wet etching have shown to be unsuitable for properly cut structures, i.e. with good dimensions control and without residues. As an alternative, plasma etching has shown great promise in this area. However, because of the highly crystalline structure of this polymer, fast etching rate, lack of residues and high aspect ratios remain hard to achieve, especially for deep etching of thick layers.