Self-assembly of liquid crystalline tetrakis(2-ethylhexyl) perylene-3,4,9,10-tetracarboxylate (C8PTC) in periodically aligned Au nanofin arrays (Au-NFs) is investigated. C8PTC forms columnar hexagonal liquid crystalline assemblies oriented parallel to the glass substrate, while the in-plane orientation of the long columnar axis is perpendicular to the surface of Au-NFs. This unique alignment reflects the interaction between the aromatic pi-surface and the bare gold surface of NFs. This work provides a new perspective to design and control molecular self-assembly confined in the designed surface nanopatterns.