It's possible that the systems are still infected by the virus. From my experience with conficker, the best way is to save the data, low level format the hard drive and reinstall or reimage the system. this may be an extreme measure but most of the security experts I've contacted suggested this action if you want to be 100% sure.
This would be my recommendation.
Please see the following McAfee KnowledgeBase article for full instructions: KB60909 - W32/Conficker.worm overview
There's a utility called KidoKiller which is very good at disinfection of conficker. Google it.
Also, if you got infected then your systems aren't patched with windows updates. You should be patching your machines to prevent infection-(you can use WSUS (free) to automatically approve critical and security patches and install them on your machines) patch them first then disinfect them to prevent reinfection. (MS08-067, MS08-068, MS09-001) We also disabled autorun on the domain (http://support.microsoft.com/kb/967715- requires pre-requisites noted in that doc) which helps quite a bit.
I still constantly see conficker /autorun worm variants getting cleaned on students and staff pen drives.
Its still out there!
Buddy, in what concerns Conficker cleaning process I think you must have a very straight step-by-step:
First of all you gotta identify the infected (memory variant) machines and for that I suggest you use the Conficker Detection Tool from McAfee/Foundstone. It´ll scan your networks´s entire range(s) in search of the P2P listening port used by Conficker.
Second, the infected machines must be patched with the KB958644. If you don´t do this all your efforts will be in vain in about 5 minutes for the machines will be infected after any disinfection no matter what.
Third, run an VS ODS, reboot the machine and run another ODS. That´s why Conficker sucks, the operational cost is way too high in order to remove it. I notice rebooting is still a more reliable way to eradicate Conficker after all.
Well, think this is it and wish you luck!