We give an overview of the open-boundary planar supercell stack method (OPSSM), as a means for treating 3D quantum transport in mesoscopic tunnel structures. The flexibility of the method allows us to examine a variety of physical phenomena relevant to quantum transport. In this work we focus on the effects of interface roughness and embedded nanostructures in tunnel devices. Four representative applications of OPSSM are discussed: (1) interface roughness in double barrier resonant tunneling structures, (2) self-organized InAs quantum dot insertions in GaAs/AlAs double barrier structures, (3) tunneling characteristics of ultra-thin oxides with interface roughness, and, (4) embedded quantum wire model of dielectric breakdown. These examples demonstrate scattering and localization effects under different biasing conditions.