The remote designation of targets in 3D complex environments, such as molecular structure, is a critical function since it is involved in numerous collaborative tasks. In fact, constrains such as depth perception and visual overload make the communication between partners very difficult and limit the understanding of the partners actions. This paper proposes a solution for the remote designation of targets in 3D complex environment. The proposed solution exploits the geometrical structure of the molecule to simplify the navigation in the 3D environment. This approach includes a haptic component to improve the selection of atoms on the molecule. Results showed an improvement of working efficiency. However, the users' feedbacks highlighted some comfort issues.