After the filters are applied, an optimization step can be performed.

In registry terms, optimizing means that the access to separate registry keys and values below a common registry key HKCU\Software\Vendor is converted to a single reference to the HKCU\Software\Vendor registry tree. In file system terms, a similar optimization applies to file and folder access below a common <AppData>\Vendor or <LocalAppData>\Vendor folder.

The Optimization Level setting controls how many key or folder levels remain after optimization. By default, both are set to 1, resulting in paths such as HKCU\Software\Vendor and <AppData>\Vendor. To manage separately multiple applications that the same vendor produces, where configuration is stored in ...\Vendor\Application\... paths, the level must be increased to 2. With this configuration, each Flex configuration file manages only the settings for a particular application.