1. A system for converting graphic representations of three dimensional molecular models into computer-aided design format, the system comprising: a processor; and a memory having a set of instructions stored thereon, wherein the instructions, when executed, cause the processor to: receive, within a chemical structure rendering application, a request identifying a three dimensional model of a chemical and/or biological structure wherein the request is one of a file save request and a print request, associate the request with conversion to a computer-aided design format, access the three dimensional model, identify a surface region of a graphic representation of the three dimensional model, convert the surface region into a polygon mesh representation, and validate the polygon mesh representation, wherein validating the polygon mesh representation comprises analyzing the polygon mesh representation to identify any inner vertices and/or mesh openings that fail to represent a single watertight wrapped surface of the polygon mesh representation of the three dimensional model.