State-of-the-art microscopy techniques (e.g., atomic force microscopy, scanning-tunneling microscopy, and optical tweezers) are sensitive to atomic-scale (100 pm) displacements. Yet, sample drift limits the ultimate potential of many of these techniques. We demonstrate a general solution for sample control in 3D using back-scattered detection (BSD) in both air and water. BSD off a silicon disk fabricated on a cover slip enabled 19 pm lateral localization precision (Deltaf = 0.1-50 Hz) with low crosstalk between axes (=3%). We achieved atomic-scale stabilization (88, 79, and 98 pm, in x, y, and z, respectively; Deltaf = 0.1-50 Hz) and registration ( approximately 50 pm (rms), N = 14, Deltat = 90 s) of a sample in 3D that allows for stabilized scanning with uniform steps using low laser power (1 mW). Thus, BSD provides a precise method to locally measure and thereby actively control sample position for diverse applications, especially those with limited optical access such as scanning probe microscopy, and magnetic tweezers.