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 on each substrate, wherein the location and the topography are determined using laser diffraction; 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, wherein the bonding includes thermally adjusting at least one of a plurality of zones on at least one of the substrates based on the topography.