Manganese doped, magnetic germanium quantum dots are predicted to be important building blocks for the future of spintronic devices. The combination of quantum confinement and carrier mediated ferromagnetism make these structures particularly interesting. The goal of this work is to understand and control the Mn environment within the Si(100), Ge wetting layer and Ge quantum dot (QD) systems and understand how it influences the magnetic properties. Samples were investigated primarily using scanning tunneling microscopy followed by magnetic analysis using a vibrating sample magnetometer and one sample with x-ray magnetic circular dichroism. An important materials question is the competition to form secondary phases in this system at elevated temperatures, particularly Mn5Ge3 and Mn11Ge8 which are both ferromagnetic (TC = 294 – 296 K). We investigate three routes for Mn doping of Ge QDs : (1) The investigation of the stability and evolution of Mn nanostructures on a Si(100)-(2x1) reconstructed surface as a function of annealing temperature up to temperatures typical for Ge QD growth. At an annealing temperature of approximately 316°C, Mn adatoms move into Si sub-surface sites and we observe an electronic effect consistent with acceptor dopants. (2) The use of a surface driven approach where Mn is deposited on the Ge QD surface and forms well-defined islands on the QD and wetting layer surface. We observed the behavior of the Mn islands during STM measurement with increasing annealing temperatures and how the islands evolved via ripening and migration across the surfaces. In addition the structure and bonding of the Mn islands specifically on the Ge {105} facets will be discussed. (3) The co-deposition of Ge and Mn throughout the Ge QD growth process. For route (3) the highest Mn concentration is 23% which results in only minor perturbations in the Ge QD growth (fewer and smaller Ge QDs), albeit secondary phases form on the surface. Lower concentration samples (5% and 8% Mn) yielded high quality quantum dots and no observable secondary phases on the surface. We presume that when secondary phases form, the majority of the Mn deposited is consumed to form the secondary phases. The competition to form secondary phases is investigated further utilizing scanning auger microscopy to map Mn and low energy electron microscopy to study the growth sequence as a function of Mn concentration. Magnetism results from one particular sample (Mn0.05Ge0.95 QD) indicate a ferromagnetic material with a Curie temperature above room temperature. We'd like to acknowledge our funding support from NSF CHE-0828318 and DMR-0907234.