A ball bonding process was simulated over a high-voltage isolation structure. The removal of an inter-dielectric metal crack-stop layer was investigated through 3D simulation. Material properties for the bonded gold ball were obtained using nanoindentation and atomic force microscopy with a methodology from the work of Ma et al. This yielded both elastic and plastic material parameters. The methodology was then evaluated by using the parameters in a nanoindentation simulation. Although the topography simulated only roughly agreed with measurement, the simulated and measured indenter curves closely overlapped. The parameters were then used in the bonding simulation. The deformation of the bond ball was also measured so that the equivalent deformation could be simulated. This was achieved following the incorporation of both ultrasonic motion and softening in the simulation. Two bonding process geometries were then set up: one with the crack-stop layer present and the other without. Both were simulated and the output was applied within a failure theory to evaluate the risk to the isolation oxide.