This chapter explores the design and assembly of nanostructured systems with inspiration from biology. Here we consider the biological inspiration as not the approach typically adopted, which is to construct synthetic materials inspired from nature. In contrast, the approach described in this chapter utilizes biological components in the assembly of smart nanostructured systems. We adapt the term “biological engineering” to describe a discipline that embodies this approach. Indeed, in 1970, this term was introduced formally with the intention to integrate engineering with biological systems to move beyond single disciplinary areas such as medicine, agriculture, or fermentation engineering. In this chapter, we further refine the discipline of “biological engineering” to be one that utilizes biological proteins, molecules, and lipids in combination with synthetic materials to assemble smart nanostructural systems. We illustrate this discipline with the assembly of nanostructured systems that are targeted for applications such as diagnostic, therapeutic, biofuel cell, or tissue enhancement/replacement in the body.