The physical and electrical properties of a silicon nanowire reconfigurable field effect transistor (RFETs) are determined by the Schottky junction between the participating phases. TEM studies on such junctions require a careful FIB‐based target preparation of thin lamellae with minimal ion‐beam induced damage. In the current study, the nickel silicide phase forming the Schottky junction with silicon is identified using EDX in the TEM, considering a calibration based on the Fourier transforms of the HRTEM micrographs of known diffraction patterns of the nickel silicide phases. The TEM lamellae are prepared using the so‐called lift‐out technique and low voltage Ga+ ion polishing to minimize the near‐surface amorphization. The structural and compositional data of the nickel silicide phase are needed for engineering the Schottky junction and corresponding theoretical modeling.