Nanoporous hard templates containing arrays of parallel, cylindrical nanopores functionalized with nanotubes as well as arrays of released, aligned nanotubes are a versatile material platform for miniaturized device components. While nanotubes of virtually any soft material can be produced by means of shape-defining nanoporous hard templates, it remains a challenge to tailor their properties by controlling the internal mesoscopic fine structure of their walls. Their supramolecular organization largely determines their mechanical, chemical, optical, and electronic properties as well as their specific surface. Hence, the rational design of the internal morphology of nanotubes will pave the way for their use as functional device components. In this chapter, recent efforts to control mesoscopic structure formation processes in the course of the preparation of nanotubes consisting of soft matter or prepared by exploiting self-assembly of soft matter will be reviewed, including the mechanisms governing the deposition of precursors and target materials into the nanopores. Specific attention will be paid to structure formation processes such as crystallization, phase separation and mesophase formation under the influence of the two-dimensional confinement imposed by the pore geometry and the interfacial interactions with the pore walls. Nanoporous hard templates allow rationally generating mesocopic fine structures in nanotubes because equilibrium and non-equilibrium states as well as unprecedented confinement-induced morphologies with new and exciting properties can be realized.