We report the fabrication of GaN lateral polarity inversion heterostructure with self assembled crystalline inversion domain boundaries (IDBs). The sample was fabricated by two step molecular-beam epitaxy (MBE) with microlithography patterning in between to define IDBs. Despite the use of circular pattern, hexagonal crystalline IDBs were self assembled from the circular pattern during the second MBE growth. Both cathodoluminescent (CL) and photoluminescent (PL) measurements show a significant enhanced emission at IDBs and in particular at hexagonal corners. The ability to fabricate self assembled crystalline IDBs and its enhanced emission property can be useful in optoelectronic applications.