Methods and apparatuses for continuous, large scale, commercially viable production of nanoforests. A roll-to-roll process passes a flexible substrate, including fibers and fabrics, through a furnace. Precursors are introduced in a growth zone in which a vertical or horizontal nanoforest of nanotubes or nanowires is grown on the substrate. Sensors and actuators with feedback control are provided for parameters such as substrate speed, substrate tension, furnace temperature, precursor flow rate, nanoforest thickness, and nanoforest. The furnace is preferably enclosed for environmental and safety purposes. The feed roll and take-up roll are disposed in housings can be attached to the furnace via airlocks, which enables rapid loading and unloading of the rolls using techniques well known in the industry while maintaining furnace conditions. The furnace can encompass flattening rollers and a second growth zone to enable manufacture of orthogonal nanoforests comprising a vertical nanoforest grown on a horizontal nanoforest.