Ordered graphene nanodisk arrays have been successfully fabricated by combining nanosphere lithography (NSL) and reactive ion etching (RIE) processes. The dimension of graphene nanodisks can be effectively tuned by varying the size of polystyrene spheres, which function as masks during RIE. Low voltage scanning electron microscopy shows that the graphene sheet could be readily patterned into periodic disk-like nanostructures by oxygen RIE. Raman mapping and spectroscopy further visualize such nanodisk arrays and reveal the nature of disks are crystalline single layer graphene. This work demonstrates an efficient and manageable way to pattern graphene. Considering the periodicity, nanometer dimension and large edge to body ratio, the graphene nanodisk arrays, such two dimensional assembly of carbon atoms offer intrisic advantages in various electronic and spintronic fabrications.