Desired enzyme nanoarrays patterned on a DNA origami scaffold were selectively isolated by affinity tag purification from a pool of differently patterned nanoarrays, and their enzymatic activity was successfully confirmed. As few as 12 histidine residues were enough to hold a huge complex of DNA origami with multiple proteins, 260 nm in length and 5.2 MDa in molecular weight, to an immobilized metal affinity resin.