The synthesis of II-VI semiconductor nanocrystals doped with transition metals has proved to be particularly difficult. In the case of CdSe quantum dots (QDs) produced via high-temperature pyrolysis in trioctylphosphine oxide (TOPO), specially designed precursors used in this study appear to be necessary to successfully incorporate low levels of Mn. A simple etching experiment and electron paramagnetic resonance (EPR) measurements reveal that most of the dopant atoms reside in the surface layers of the inorganic lattice. The dopant dramatically affects Cd-113 magic angle spinning (MAS) nuclear magnetic resonance NMR spectra; the observed paramagnetic shift and decreased longitudinal relaxation time are consistent with Mn incorporated in the QDs. Paramagnetic atoms in QDs generate large effective magnetic fields, which implies that magnetooptical experiments can be performed simply by doping. Results from fluorescence Line narrowing (FLN) studies on Mn-doped CdSe QDs mirror previous findings on undoped QDs in an external magnetic field. Experimental fitting of photoluminescence excitation (PLE) spectra of doped QDs reveals that the effective absorption line shape contains a new feature that is believed to be a previously unobserved but theoretically predicted, optically dark fine structure state.