In theory, you could do it with Netfabb, but there are a lot of shapes where it's just not worth the effort.
Try uploading your model to cloud.netfabb.com and see what it comes back with .. it often fixes many of my issues.
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If your model has one main shell, it's possible that the extra shells are 'trash' that is not relevant to the overall design.
In Netfabb, enter Repair mode.
Right click the main shell and choose the option "Select this shell"
Then, right click again, and choose "Remove selected triangles"
That will delete the main shell, and you can see what might be left floating.
If you determine that you don't need those floating peices, you can just delete the Repair - !don't apply it! and get back to your base model.