The magnetic doping of semiconductor materials is a critical contribution to the development of novel spintronics device structures. Mn-doping of group IV semiconductor materials is highly desirable for seamless combination of spin- and charge driven electronics. One of the critical limiters is currently the development of a suitable material, where Mn is placed in the correct bonding state, and not in germanide or silicide compounds. The main goal of our research is to develop a fundamental understanding of the relation between atomic-level bonding and the magnetic signature of the system. We combine STM (scanning tunneling microscopy) observations of material synthesis with measurement of the integral magnetic properties with magnetometry and XMCD (x-ray magnetic circular dichroism, Advanced Light Source). We studied the following systems: (A1) Mn-nanowires on Si(100) and their response to annealing, (A2) delta-doped Mn as Si-Mn-Si and Si-Mn-Ge synthesized from (A1), (B1) Ge-quantum dots (QD) doped by surface-deposition of Mn, and (B2) co-deposition of Mn during Ge QD growth. All growth processes were analyzed by STM, and we therefore possess atomic level information about the structure of Mn and the semiconductor matrix. Monoatomic Mn-wires (A1) form on the reconstructed Si(100) surface and are always oriented perpendicular to the dimer rows of the Si-surface. They are therefore an ideal vehicle for the fabrication of delta-doped Mn-layers, which are embedded within a semiconductor matrix (A2). The quality of Mn-wires is controlled by the density of defects on the surface. A phase diagram for wire growth has been established, and Monte-Carlo simulations are used to unravel the role of surface defects. The subsequent growth of the Si and Ge caps does not modify the Mn-wires. Mn-doping of Ge QDs has recently attracted considerable attention, and we will discuss the growth processes for (B1) and (B2) with special attention to the role of temperature, and bonding configuration with Mn. The development of the wetting layer and QD growth is only marginally influenced by the presence of Mn. Deposition of Mn on the QDs leads to roughening of the wetting layer surface, and formation of Mn-islands on the QD facets. The magnetic signature of structures (A2), (B1) and (B2) show either superparamagnetic behavior or a very narrow ferromagnetic loop. We will compare the magnetic data (saturation magnetization, spin and orbital moments, bonding configuration) across all nanostructures. C. Nolph and K. Simov performed the work in equal parts, and we collaborated with C. Jenkins and P. Glans for the XMCD measurements. The authors gratefully acknowledge the support by NSF awards CHE-0828318 and DMR-0907234. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.