Electrically insulated carbon nanotube (CNT) based separation columns have been fabricated that can withstand an electrical field strength of more than 2.0 kV cm⁻¹ without bubble formation from electrolysis. The carbon nanotubes were grown in a pillar array defined by photolithographic patterning of the catalyst layer used for synthesis of the nanotubes. Multiwall carbon nanotubes are inherently electrically conductive and cannot be used as a continuous layer in the microfluidic channels, without short circuiting the electrical field in the separation column, when the field strength is more than a couple of 100 V cm⁻¹. Here, the carbon nanotubes are grown in an array of hexagonal pillars, where the nanotubes in the individual pillars are not in direct electrical contact with the nanotubes of the adjacent pillars. This makes it possible to increase the electrical field strength from around 100 V cm⁻¹ to more than 2.0 kV cm⁻¹ and thereby to use the CNT columns for electrokinetic separations with the high electrical field strengths that are typically used in this application. An electrochromatographic separation of two Coumarin dyes was demonstrated on the CNT column with an acetonitrile content of 90%.