Focused ion beam patterning is a powerful technique for guiding the growth of ordered hexagonal porous anodic alumina. This study shows that, with the guidance of the focused ion beam patterning, hexagonal porous anodic alumina with interpore distances from 200 to 425 nm can be fabricated at 140 V in 0.3 M phosphoric acid. When the interpore distance is increased to 500 nm, alternating diameter nanopore arrays are synthesized with the creation and growth of new small pores at the junctions of three large neighboring pores. Moreover, alternating diameter nanopore arrays in hexagonal arrangement are fabricated by focused ion beam patterning guided anodization. Interpore distance is an important parameter affecting the arrangement of alternating diameter nanopore arrays. Different types of novel patterns are obtained by designing different focused ion beam concave arrays. The fundamental understanding of the process is discussed.