The work reported herein demonstrated that nanopipes can be formed via a surfactant effect, in which boron impurities preferentially migrate to semipolar and nonpolar facets. Approximately 3 μm-thick GaN layers were grown using halogen-free vapor phase epitaxy. All layers grown in pyrolytic boron nitride (pBN) crucibles were found to contain a high density of nanopipes in the range of 1010 to 1011 cm−2. The structural properties of these nanopipes were analyzed by X-ray rocking curve measurements, transmission electron microscopy, and three-dimensional atom probe (3DAP) tomography. The resulting 3DAP maps showed nanopipe-sized regions of boron segregation, and these nanopipes were not associated with the presence of dislocations. A mechanism for nanopipe formation was developed based on the role of boron as a surfactant and considering energy minima. A drastic reduction in the nanopipe density was achieved upon replacing the pBN crucibles with tantalum carbide-coated carbon crucibles. Consequently, we have confirmed that nanopipes can be formed solely due to surface energy changes induced by boron impurity surface segregation. For this reason, these results also indicate that nanopipes should be formed by other surfactant impurities such as Mg and Si.