A method, a system and a computer readable medium having a set of instructions stored thereon for die-to-robot alignment for die-to-substrate bonding are described. First, a robot is aligned with a substrate to provide a pre-aligned robot. Next, a die is aligned with the pre-aligned robot to provide a robot-aligned die. Finally, the robot-aligned die is bonded to a region of the substrate. The substrate is held stationary immediately following the aligning of the robot with the substrate and at least until the robot-aligned die is bonded to the region of the substrate.