The clean machine is inspected for every aspect of its configuration in both files and registry settings. This scan is initiated by the admin and logically could take a while to complete considering the amount of actions needed to get a good inspection of the base system. Once that first step has completed, the software that is to be deployed is installed on the example computer. At that point, a second inspection is performed by the msi creator to allow it to realize all the changes made by the software that you have installed in the interim. The msi creator will create an installation package that incorporates all the files added by the program you installed as well as instructions needed to make the registry and configuration changes needed on the system for the software to function. It is in this way that an msi creator can generate a package for almost any piece of software.