The existing Ar plasma sputter cleaning and dilute HF dip wet cleaning techniques have drawbacks, including critical dimension change, plasma damage, poor selectivity to oxides, vacuum breakage (causing oxide formation), and queue-time control. Siconi cleaning, a newly developed cleaning process for pre-Ni silicide cleaning at 65 nm, enables superior cleaning performance, including (1) selective removal of native oxide to minimize loss of Si and Ni, (2) elimination of spikes and reduction of pipe defects at the NiSi/Si interface, and (3) elimination of the queue-time dependency for improved productivity and simplification of fabrication. In this study, the chemical mechanism, hardware configuration, and Siconi integration results are described. The formation mechanisms for both spike and pipe defects are discussed, and practical solutions to these problems are addressed in detail. A significant reduction in junction leakage current, by three orders of magnitude, was observed. In addition, the pipe defect at the wafer edge is described and discussed.