Nanopipes are 1-nm-wide open pores that extend through the entire thickness of epitaxial NaCl-structure transition-metal nitride layers. They form due to a combination of anisotropic surface diffusion and atomic shadowing effects. Their shape, orientation, and arrangement can be controlled by ion-irradiation and deposition angles. CrN, TaN, ScN, and TiN layers were grown on MgO(001) at 600-1000 °C by ultra-high-vacuum magnetically-unbalanced magnetron sputter deposition in pure N@sub 2@ and N@sub 2@+Ar discharges at 3-20 mTorr. These deposition conditions result in a highly anisotropic surface diffusion with hop-rates that are 7 orders of magnitude smaller on (111) versus (001) surfaces. This anisotropy leads, during growth under limited adatom mobility conditions, to kinetic surface roughening and the development of deep surface cusps which cause atomic shadowing and the formation of nanopipes that are elongated along the [001] growth direction. The nanopipes have rectangular cross-sections and form self-organized arrays aligned in orthogonal [100] and [010] directions, precisely replicating the in-plane correlation of the surface morphology. Non-normal deposition increases the level of atomic shadowing and introduces a controlled tilt to the nanopipes. Increasing the N@sub 2@@super +@-ion irradiation flux or decreasing the N@sub 2@ partial pressure (and, hence, the steady-state N coverage) during growth provides a corresponding increase in cation surface mobilities leading to smoother surfaces, less atomic shadowing, and partial or full suppression of nanopipe formation.