We employ Electron beam induced deposition (EBID) in combination with autocatalytic growth (AG) processes to fabricate magnetic nanostructures with controllable shapes and thicknesses. Following this route, different Fe deposits were prepared on silicon nitride membranes under ultra-high vacuum conditions and studied by scanning electron microscopy (SEM) and scanning transmission x-ray microspectroscopy (STXM). The originally deposited Fe nanostructures are composed of pure iron, especially when fabricated via autocatalytic growth processes. Quantitative near-edge x-ray absorption fine structure (NEXAFS) spectroscopy was employed to derive information on the thickness dependent composition. X-ray magnetic circular dichroism (XMCD) in STXM was used to derive the magnetic properties of the EBID prepared structures. STXM and XMCD analysis evinces the existence of a thin iron oxide layer at the deposit-vacuum interface, which is formed during exposure to ambient conditions. We were able to extract magnetic hysteresis loops for individual deposits from XMCD micrographs with varying external magnetic field. Within the investigated thickness range (2-16 nm), the magnetic coercivity, as evaluated from the width of the hysteresis loops, increases with deposit thickness and reaches a maximum value of ∼160 Oe at around 10 nm. In summary, we present a viable technique to fabricate ferromagnetic nanostructures in a controllable way and gain detailed insight into their chemical and magnetic properties.