% sudo rm -rf /Library/Java/JavaVirtualMachines/1.6.0*.jdkĭo NOT remove any content in the amework (Note.: It under /System/Library/Frameworks/amework ) % sudo rm -rf /System/Library/Java/JavaVirtualMachines/1.6.0.jdk Remove the 'system' JVM installed and maintained by Software Update However if you wish to rid your machine of Java SE 6,

The security issues are invariably sandbox violation tricks, and the standalone apps aren’t running Java sandboxed anyway.

The security issues aren’t going to impact these apps. Java 6 is on your machine for legacy software that relies on it in standalone applications. But you can’t use Java 6 on the web anyway. Security updates are important because of web sites that use Java maliciously. I don’t know the answer to your question, but I can suggest that you might be causing yourself unneeded problems. From The macosx-port-dev Archives and How to properly uninstall Java 6 on OSX?: