Carbon nanotubes (CNTs) are ideal candidates as electrode materials for neuronal stimulation and monitoring devices such as microelectrode arrays (MEA). They provide a high charge injection limit without significant Faradic reactions and carbon nanotube electrodes have a high surface area to volume ratio. Flexible MEAs typically consist of thin conductors buried in a flexible insulator such as polyimide, where the actual contact areas have been opened by dry etching of the polyimide. CNTs are positioned in these contact areas by a low temperature (350 ◦C) chemical vapour deposition process from a catalyst which was deposited on the contact in the polyimide recess. To overcome poisoning of the catalyst by outgassing from the sidewalls of the polyimide trenches even at such low temperatures, a pre-treatment of the catalyst in an ammonia atmosphere for 15 min at 40 mbar and 350 ◦C was introduced. CNT growth on identical structures made from polyimide and silicon is compared in order to identify the relevant issues affecting growth.