The capacity to create an increasing variety of bioactive molecules that are designed to assemble in specific configurations has opened up tremendous possibilities in the design of materials with an unprecedented level of control and functionality. A particular challenge involves guiding such self-assembling interactions across scales, thus precisely positioning individual molecules within well-organized, highly-ordered structures. Such hierarchical control is essential if peptides and proteins are to serve as both structural and functional building blocks of biomedical materials. To achieve this goal, top-down techniques are increasingly being used in combination with self-assembling systems to reproducibly manipulate, localize, orient and assemble peptides and proteins to form organized structures. In this tutorial review we provide insight into how both standard and novel top-down techniques are being used in combination with peptide or protein self-assembly to create a new generation of functional materials.