A new surface cleaning technique, the CF4Cleaning Process (CFCP), is proposed for the fabrication of Nb and Nb-based Al5 compound tunnel junctions with native oxide barriers. The effects of fabrication conditions and these superconducting material properties on the characteristics of these junctions with Pb or Pb alloy counterelectrodes are investigated. High-quality junctions with a well-defined gap, no knee and very low excess conductance are successfully fabricated through the conventional lift-off technique for Al5 compounds (Nb3Al, Nb3Ge and Nb3Si) as well as Nb. Arrays of 100 series-connected 2 μmφ Nb/Pb-Bi Junctions are fabricated with the standard deviation (σ) of critical current (Jc= 15.1 KA/cm2) equal to 2.5 %. The CFCP mechanism that contributes to the formation of such good junctions is studied using in-situ X-ray photoelectron spectroscopy (XPS). Chemical shifts of the Nb 3d levels on the CF4plasma-cleaned Nb surfaces indicate the presence of an Nb-F layer. These XPS spectra show that the tunnel barrier is composed of mixed Nb2O5and Nb-FO compounds.