Inspired by the biochemical reactions that often occur in confined nanocompartments, e.g., organelles, various artificial biomimetic nanostructures have been synthesized for studying confinement effects in natural biochemical processes. Among these systems, protein-based nanotubes are attracting an increasing interest due to their many potential applications. In this context, the thesis focuses on the construction of tubular enzyme-rich nanocylinders by templated layer-by-layer assembly in nanoporous membranes. After removal of the sacrificial templates, free tubular nanotubes incorporating enzymes are obtained; these can be considered as one step towards artificial biocatalytic organelles. We first investigate how to synthesize stable enzyme nanotubes of high activity. When prepared in optimized assembly conditions, robust enzyme LbL-nanotubes are obtained with improved resistance towards the detemplating process. Afterwards, we devise a novel collection strategy, namely adjuvant-assisted filtration, able to extract LbL-nanotubes from the template membrane and to redisperse them with minimal aggregation in an aqueous medium. The tubular structure and biological activity of the collected enzyme nanotubes are retained in aqueous dispersion, demonstrating the robust capability of our methodology to recover template-synthesized nanotubes for biological applications. Finally, the fabrication of a ‘paper’ mat made of LbL-nanotubes is demonstrated. The structure of the resulting mats is investigated by SEM and AFM, showing the possibility of construction of tailored nanofibrous scaffolds comprising nanotubes incorporating functional components. This methodology thus provides a new and general way to create smart nanofibrillar scaffolds, which offers exciting opportunities for applications in, e.g., tissue engineering, biosensing, and bio-purification.