An array of carbon nanotubes is prepared by exposing a catalyst structure to a carbon nanotube precursor. Embodiment catalyst structures include one or more trenches, channels, or a combination of trenches and channels. A system for preparing the array includes a heated surface for heating the catalyst structure and a cooling portion that cools gas above the catalyst structure. The system heats the catalyst structure so that the interaction between the precursor and the catalyst structure results in the formation of an array of carbon nanotubes on the catalyst structure, and cools the gas near the catalyst structure and also cools any carbon nanotubes that form on the catalyst structure to prevent or at least minimize the formation of amorphous carbon. Arrays thus formed may be used for spinning fibers of carbon nanotubes.