This paper presents a new system using a haptic device with an automatic molecular docking and assembly search method for the problems of molecular docking and molecular assembly in computer-aided molecular design (CAMD). The developed haptic force-torque feedback provides the users an intuitive tool for understanding the interactions among molecules while an automatic docking and assembly search method, NanoDAS, assists the user on determining the docking and assembly feasibility. The proposed system can be used as a tool to screen out candidate molecules that are infeasible, in terms of geometry and energy, to dock or assemble into a larger molecule. This identification of feasible molecules can significantly improve and accelerate the discovery and design of new pharmaceutical drugs and nanoscale devices in CAMD. Computer implementation and illustrative examples are also presented in this paper.