The natural world provides numerous cases for analogy and inspiration in engineering design. Biological organisms, phenomena and strategies, herein referred to as biological systems, are, in essence, living engineered systems. These living systems provide insight into sustainable and adaptable design and offer engineers billions of years of valuable experience, which can be used to inspire engineering innovation. This research presents a general method for functionally representing biological systems through systematic design techniques, affording conceptualization of biologically-inspired, engineering designs. Functional representation and abstraction techniques are utilized to translate biological systems into an engineering context. Thus, the biological system information is accessible to engineering designers with varying biological knowledge, but a common understanding of engineering design methods. Functional modeling is typically driven by customer needs or product re-designs; however, these cannot be applied to biological systems. Thus, we propose the use of biological category and scale to guide the design process. Mimicry categories and scales, in addition to answering a design question, aid the designer with defining boundaries or scope when developing a biological functional model. Biological category assists with framing the information in the right perspective, where as, biological scale deals with how much detail is required for an adequate representation of the biological system to utilize the information with a chosen engineering design method. In our case, the engineering design method is function-based design. Choosing a category serves to refine the boundary, but, like scale, its consideration might prompt the designer to consider the same biological system in a new and unique way leading to new ideas. General guidelines for modeling biological systems at varying scales and categories are given, along with two modeling examples.