Custom tooling is an effective method to improve surface roughness, geometrical accuracy, machining efficiency, and consequently the core competitiveness of the final products in very complicated freeform creation and micro/nano machining, such as the propeller, blisk and ductile-mode machining of hard and brittle materials. However, commercially available CAM systems have limitations in generating CNC programs for these customized tools due to considerations for special custom tool fabrication processes. Therefore unique CAM system is needed and consequently dedicated CAD sub-system is the prerequisite for such CAM system. In this paper, the dedicated CAD sub-system design is studied to extend the authors’ previous study. The characteristics of customized tools are summarized and analyzed. Then, the functions for the dedicated CAD sub-system are analyzed and defined. Finally, the system is designed and developed by using VC++, Open CASCADE, and ActiveX Data Object techniques.