I know how to add exceptions from blocking, but how can I add exception for scanning in Avira?
You need to enable Expert Mode in order to gain access to the exclude options. You can do this from the Settings menu in Avira (versions 12 and 13).
After that, use the following paths to add files to exclusion:
System Scanner → Scan → Exception
Real-Time Protection → Scan → Exception
For additional information, use the following support page: http://www.avira.com/en/support-for-business-knowledgebase-detail/kbid/900