In Silicon-Germanium/Si(001) heteroepitaxy and during ion-bombardment of semiconductor surfaces, the mechanisms of self-organisation are used to generate nanostructures. This is a rather elegant way to create regular arrangements of nanostructures on the wafer-scale. The nanostructures were characterized using the Atomic Force Microscope (AFM). Besides nanofaceted SiGe structures, noble-gas ion-bombardment of Si(001) surfaces resulted in nanostructures which extend 30 nm in diameter and 3,5 nm in height. The self-organised semiconductor-substrates were used as templates to deposit magnetic layers in order to generate regular arrays of independent nanomagnets. On {113} faceted SiGe surfaces, the shadow deposition of Co resulted in a regular arrangement of nanomagnets which are 200 nm x 100 nm small. The nanomagnets where characterized by x-ray photo-emission electron microscopy (XPEEM) analysing the x-ray magnetic circular dichroism (XMCD). By shadow-deposition on ion-eroded GaSb-surfaces nanomagnets were created, which have a diameter of 50 nm. They were detected with the magnetic force microscopy (MFM). With this technique a storage density of about 0.2 Tbit/square inch can be reached. The method of shadow deposition on self-organised semiconductor templates is a proper tool for the upcoming development of storage media with increasing storage density.