This paper describes a case study representing the design essence of a prototype ultra-high vacuum artifact transport system (ATS) in an existing design repository (DR). Specifically designed for the purpose of transporting nanometer-scale dimensional artifacts at pressures near 10−8 Pa, the ATS consists of a transport cart and an ultra-high vacuum (UHV) system. The artifacts are the result of nanomanufacturing efforts to create atom-based dimensional standards for the semiconductor industry. To populate the design repository, we represent engineering geometry, function and associated behavior, as well as taxonomies of generic functions and flows of the transport system. We model geometry with digital photographs and Virtual Reality Markup Language (VRML) images of actual Computer-aided Design (CAD) drawings, represent function with linked textual descriptions, and capture behavior with mathematical expressions. Through an evolving user interface, this representation serves to capture the more than 50 parts and systems of the ATS in such a way that the information relating to form, function and behavior is accessible and browsable to subsequent designers. We conclude that such a representation, or ones similar to it, can provide the basis for a generic database in which specific information — including design rationale — can be easily retrieved by future design teams.