The wafer bonding process becomes a flexible approach to material and device integration. The bonding strength in 3-dimensional process is crucial factor in various interface bonding process such as silicon to silicon, silicon to metals such as oxides to adhesive intermediates. A measurement method of bonding strength was proposed by utilizing AFM applied CNT probe tip which indicated the relative simplicity in preparation of sample and to have merit capable to measure regardless type of films. Also, New Tool was utilized to measure of tip radius. The cleaned $SiO_2$-Si bonding strength of SPFM indicated 0.089 $J/m^2$, and the cleaning result by RCA 1($NH_4OH:H_2O:H_2O_2$) measured 0.044 $J/m^2$, indicated negligible tolerance which verified the possibility capable to measure accurate bonding strength. And it could be confirmed the effective bonding is possible through SPFM cleaning.