Aluminium anodization under optimized conditions can naturally generate close-packed and aligned nanopore arrays, but the spatial extent of such regular pore arrangement is generally limited. Here we demonstrated the use of soft ultraviolet nanoimprint lithography to guide the formation of nanopores at specific locations, using an elastomer negative mold for the process. By anodizing at voltages which naturally led to the formation of pores with matching averaged interpore separation, pre-patterned triangular holes (diameter 100 nm, periodicity 350 nm) on aluminium thin films induced conformal growth of nanopores at pre-defined positions. In addition, pores in geometries other than close-packed patterns were prepared, with square pore arrangement being demonstrated in this work. The influence of the anodization voltage on the final pore formation was also studied. Our results illustrated the possibility to fabricate well-organized nanopore arrays with conditions far less stringent than those reported in literature, which has the potential to be adopted for applications where regular pore alignment are critical.