Certificate Backup

I am looking to backup all certificates installed on a desktop and move them over to the users new desktop via a script. I can't rely on the users knowing if they have a cert or backing it up themselves. I don't want to manually backup 1000's of pcs.

I looked at certmgr.exe but it does not allow the use of put and all options at the same time. Is anyone aware of any other utilities or ways to go about this?