We report on the isolation of single negatively-charged-silicon-vacancy (Si-V-) centers in nanodiamonds. We observe the fine structure of single Si-V-centers with reduced inhomogeneous ensemble linewidth below the excited-state splitting, stable optical transitions, good polarization contrast, and excellent spectral stability under resonant excitation. On the basis of our experimental results, we develop an analytical strain model where we extract the ratio between strain coefficients of excited and ground states as well the intrinsic zero-strain spin-orbit splittings. The observed strain values are as low as the best values in low-strain bulk diamond. We achieve our results by means of H-plasma treatment of the diamond surface and in combination with resonant and off-resonant excitation. Our work paves the way for indistinguishable, single-photon emission. Furthermore, we demonstrate controlled nanomanipulation by an atomic-force-microscope cantilever of one-A nd two-dimensional alignments with an accuracy of about 10 nm, as well as new tools including dipole rotation and cluster decomposition. Combined, our results show the potential to utilize Si-V-centers in nanodiamonds for controlled interfacing via optical coupling of individually-well-isolated atoms for bottom-up assemblies of complex quantum systems.