The self-assembly of soluble proteins into amyloid aggregates is a mechanism which can be observed in processes that are functional or disease-associated. The resulting fibrillar structures can be formed from a variety of different proteins, but all share a β-sheet rich architecture and a variety of remarkable optical and mechanical properties. Their disease association makes amyloids relevant for medical research, but the characteristic structure and associated properties have also led to an interest in harnessing them as building blocks for functional materials. This thesis presents the development of methods for the study and manipulation of amyloid self-assembly. Currently, techniques for patterning and controlled deposition of the aggregates are lacking, which limits a wider use of the material. The first part of this thesis therefore introduces a method to pattern amyloids into arbitrary structures with macroscale order, while maintaining their characteristic properties. β-lactoglobulin proteins are electro spun into free-standing and surface deposited fibres with micron diameter and centimetre length. Structural, mechanical, and optical characterisation methods are used to demonstrate the fibres’ high mechanical strength, as well as the fluorescent and light-guiding properties of the material. This new, optically active, and strong biomaterial has potential for applications in interconnected photonic and bioelectronic devices. The second part of this thesis presents the design and implementation of a structured illumination microscope (SIM) system, which can be used for the study of pathological amyloids and their effects on fast processes in living cells. By utilising a single galvo scan mirror for interferometric pattern formation, as well as a multichannel detection system, the instrument becomes faster, achromatic, and more flexible for adaptation to different imaging requirements than previous implementations of SIM. The resolution enhancement and the multi-channel capabilities of the instrument are demonstrated in up to three colours simultaneously on a variety of test samples. Due to its simple and cost-efficient design, the instrument is envisaged to make SIM available to a wider range of studies on pathological amyloids.