If you are sure you have removed all malware, you should remove restore points as some will be infected.
It is also a good idea to clean temporary files and logs, too.
Turn off system restore. This will remove all restore points since some are infected . Turn system restore back on. http://www.real-knowledge.com/flushres.htm
Remove temporary files, logs, cookies, etc. by using Ccleaner. Do not use "Advanced Settings" or the "Issues" button. Use only the default settings. http://www.ccleaner.com/