1. A method of bonding two circuitry-including substrates, the method comprising: providing a first stage for holding a first circuitry-including substrate and a second stage for holding a second circuitry—including substrate; identifying an alignment mark on each substrate; determining a location and a topography of each alignment mark; creating an alignment model for each substrate based on the location and topography of the alignment mark thereon; and bonding the first and second circuitry—including substrates together while aligning the first and second substrates based on the alignment model.