The present invention relates to a method for fabricating columnar or lamellar structures of organic molecules aligned into a large-area single domain, and more particularly, to a method for fabricating columnar or lamellar structures of organic molecules aligned into a large-area single domain, in which organic molecules having a random alignment due to their poly-domain structure are spatially confined between a bottom substrate and a top substrate, and then heated above the isotropic transition temperature of the organic molecules, thereby allowing the organic molecules to have a new alignment different from the initial alignment. Columnar or lamellar structures of organic molecules aligned into a large-area single domain, which are fabricated by the fabrication of the present invention, are large-area single domains having a perfectly columnar shape. Also, because the organic molecules are spatially confined between flat substrates regardless of the properties of the substrates and are subjected to a heat-treatment process, the fabrication method according to the present invention enables nanostructures to be formed in a rapid and efficient manner compared to alignments methods employing high temperatures or solvents.