Self-assembled iron-silicide nanostructures were prepared by reactive deposition epitaxy of Fe onto silicon. Capacitance-voltage, current-voltage, and deep level transient spectroscopy (DLTS) were used to measure the electrical properties of Au/silicon Schottky junctions. Spreading resistance and scanning probe capacitance microscopy (SCM) were applied to measure local electrical properties. Using a preamplifier the sensitivity of DLTS was increased satisfactorily to measure transients of the scanning tip semiconductor junction. In the Fe-deposited area, Fe-related defects dominate the surface layer in about 0.5 μm depth. These defects deteriorated the Schottky junction characteristic. Outside the Fe-deposited area, Fe-related defect concentration was identified in a thin layer near the surface. The defect transients in this area were measured both in macroscopic Schottky junctions and by scanning tip DLTS and were detected by bias modulation frequency dependence in SCM.