The surface morphologies of nanopipes were imaged using a scanning electron microscope and an atomic force microscope in undoped AlGaN epilayers grown by metal organic vapor phase epitaxy on GaN-based layers, The nanopipes usually appear as dodecagonal and hexagonal pyramidal indentations for larger and smaller sizes, respectively, with a pinhole at each of their centers. The results indicate that {1 1 (2) over bar 1} facets may play an important role as well as {1 0 (1) over bar 1} facets during the nanopipe formation in undoped AlGaN epilayers, Energy dispersive X-ray spectroscopy shows that Al atoms have precipitated more distinctly on the facets of the nanopipes. The image of yellow cathodoluminescence is characterized by a bright ring around the outer region of pyramidal indentations. This is suggested to be a result of competition between the higher concentration of the defects responsible for the yellow luminescence and the thinner epilayer in the facet site.