We present the fabrication of lipid nanoscaffolds inside carbon nanotube arrays by employing the nanostructural self-assembly of lipid molecules. The nanoscaffolds are finely tunable into model biomembrane-like architectures (planar), soft nanochannels (cylindrical) or 3-dimensionally ordered continuous bilayer structures (cubic). Carbon nanotube arrays hosting the above nanoscaffolds are formed by packing of highly oriented multiwalled carbon nanotubes which facilitate the alignment of lipid nanostructures without requiring an external force. Furthermore, the lipid nanoscaffolds can be created under both dry and hydrated conditions. We show their direct application in reconstitution of egg proteins. Such nanoscaffolds find enormous potential in bio- and nano-technological fields.