The present disclosure is directed to a high throughput clip bonding tool or system which is flexible and easily adapts to different clip bond pitches or sizes. The clip bonding system may be an integrated system with various modules, including a clip singulation module, a feeder module, a transfer module and a clip attach module within a shared footprint. For example, an incoming clip source may be fed to the clip singulation module for clip singulation before the singulated clips are transferred by the feeder and transfer modules to a clip presentation area for clip alignment before pickup. A pickup tool of the clip attach module is configured to facilitate pickup and attachment of clips onto the semiconductor packages to be clip bonded. For example, the pickup head is programmable to facilitate clip bonding process of different applications which may require clips and packages with different sizes.