Manipulation of micro-nano materials inside an electron microscope requires accurate position control of the micromanipulators and precise management of the forces involved in the manipulation process. While visual data is vital for object tracking and path planning, incorporating force feedback is critical for ensuring controlled physical interactions. Relying solely on visual feedback to execute any experimental task on nanomaterials is inadequate. Since human operators are more adaptable to force changes than robotic systems, developing bilateral controllers is essential for precise human intervention in nanorobotic-based experimental tasks. Therefore, a bilateral SEM-based nanorobotics system with haptic feedback has been developed for multi-scale manipulation. Adding haptic feedback to these tasks enhances manipulation precision and reduces completion time as well as the mean force exerted on the object. This work also introduces a new user interface for 3D modeling and haptic interactions.