My testing of v3.9.95478.509 indicates that a file can be excluded from AV detection by either adding it to the Exclusions list under Virus Scanner Settings or adding to to My Own Safe Files under Defense+. My personal strategy is to put individual files in My Own Safe Files, and to put directories or extension groups in the Exclusions list.
When the AV real-time scanner detects malware, the options offered today are:
Ignore - Once
Ignore - Add to My Own Safe Files
Ignore - Add to Exclusions
When the AV manual scanner detects malware, the options offered today for individual files are:
I request that extra Ignore options from the real-time scanner are offered for the manual scanner.