The James Webb Space Telescope (JWST) is a segmented deployable telescope, utilizing 6 degrees of freedom for adjustment of the Secondary Mirror (SM) and 7 degrees of freedom for adjustment of each of its 18 segments in the Primary Mirror (PM). When deployed, the PM segments and the SM will be placed in their correct optical positions to within a few mm, with accordingly large wavefront errors. The challenge, therefore, is to position each of these optical elements in order to correct the deployment errors and produce a diffraction-limited telescope, at λ=2μm, across the entire science field. This paper describes a suite of processes, algorithms, and software that has been developed to achieve this precise alignment, using images taken from JWST’s science instruments during commissioning. The results of flight-like end-to-end simulations showing the commissioning process are also presented.