The design of CAD tools for nanofabrics involves new challenges not encountered with conventional CMOS technology. In this paper, we describe the design of a prototyping CAD tool targeting design automation of applications on a wide range of nanofabrics. Our proposal is based on a variety of models that capture as well as isolate the differences between the fabrics. This tool supports the design flow from behavioral description to final layout. It integrates fault-tolerant techniques and fabric-related density transformations with more conventional design automation techniques. After an overview of common requirements, physical models, and associated techniques, a case study in the context of NASIC fabrics is used to illustrate some of the concepts.