There are three approaches to this:

1. Use SPSiteManager Utility which is written by Keith Ritchie and
available as free download on his blog. This is a command based utility
and given 'as is' so you need to compile and run it on the SharePoint
Server.

2. As mentioned in the SDK, run 3 consequtive full crawls (I presume
you have tied the file  share to non portal content)on non portal to
remove these results.

3. Reset the index! this is fastest but a cheesy solution.