This paper presents the effect of BCB sealing ring flatness on BCB bonding for wafer-scale BCB cap transfer packaging. BCB sealing ring has shown partial bonding or full bonding depending on its flatness. It is found that the principal cause of the partial bonding is due to non-flat BCB sealing ring caused by multilayer BCB coating process. As a solution, BCB dry etching has been proposed to improve the flatness of the BCB sealing ring for full BCB bonding. Besides, partial bonding of BCB ring has been analyzed through FEM modeling of BCB cap with a non-flat sealing ring. The FEM model consists of Si carrier wafer, BCB cap, and Si target substrate. Unique load is applying pressure on top of Si carrier wafer like wafer-scale bonding. The role of applying pressure is to get BCB sealing ring to be contacted and expand bondable area with target Si substrate. As BCB sealing ring is bonded through BCB polymerization by holding the pressure for 1 h at 250 °C, mechanical properties of virgin BCB sealing ring has been changed during bonding. Thus, it has been chosen as variable for parametric analysis. Also, BCB cap dimension has been used as another parameter for the parametric analysis.