Prepping a Windows PE build environment removes any components that are present in the component store but have not been installed. This shrinks the size of your Windows PE image, but it also has the effect that you will no longer be able to service the image. Once you've determined that your Windows PE build environment is ready to be captured as an image (.wim file) you can prep your build environment using Peimg like this:
Peimg /prep c:\winpe_x86\base
After your build environment is prepped, you can capture an image of your build environment using the imagex command.
For more information on deploying Vista, see my series of articles titled Deploying Vista on WindowsNetworking.com, and see also Part 2: Deployment in the Windows Vista Resource Kit, Second Edition from Microsoft Press.