When you capture, you can log out the tape and create a capture list of only the good clips...that would help a lot, not to mention make the media more manageable.
If all the media is in there, then I would do a quick timeline chop on the reel and cut out everything that you KNOW you won't need and use the project manager to trim the project. The trimmed media will be created in a new folder and you can delete the original files.