  We report on the isolation of single SiV$^-$ centers in nanodiamonds. We
observe the fine-structure of single SiV$^-$ center with improved inhomogeneous
ensemble linewidth below the excited state splitting, stable optical
transitions, good polarization contrast and excellent spectral stability under
resonant excitation. Based on our experimental results we elaborate 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 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 nano-manipulation via atomic force
microscope cantilever of 1D- and 2D-alignments with a so-far unreached accuracy
of about 10nm, as well as new tools including dipole rotation and cluster
decomposition. Combined, our results show the potential to utilize SiV$^-$
centers in nanodiamonds for the controlled interfacing via optical coupling of
individually well-isolated atoms for bottom-up assemblies of complex quantum
systems.
