This paper deals with the problem of finding a compromise between stability and transparency for bilateral haptic control in nanorobotics. While manipulating objects with an AFM, real time visual feedback is not available. Force feedback is used to compensate for this lack of visual information. The structure of the control scheme and the value of the controller gains are critical issues for stability, transparency, and ease of manipulation. Two common control schemes are analyzed for submicron scale interactions. Based on stability and transparency criteria, the influence of each of the controllers' gains is derived. The applications for which the bilateral couplings are best suited, as well as their intrinsic limitations are discussed. The theoretical analysis is validated with an experiment composed of several phases with high dynamic phenomena.