Aligned carbon nanotubes with uniform outer diameters, ordered over wafer-scale areas were fabricated using porous alumina templates on silicon. Anodization of aluminium films deposited on corrugated silicon surfaces, patterned using interference lithography, led to periodic pore structures over wafer-scale areas with controlled spacing and symmetry, and with pore sizes independently controlled through the anodization conditions. Nickel deposited at the base of the pores catalysed CNT growth during PECVD. These results demonstrate a wafer-scale approach to the control of the size, pitch, ordering symmetry, and position of nanotubes and nanowires in a rigid insulating scaffold.