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Ouch, yeah... well, the first thing you can do is check the .fpe file and make sure that "transparency=" has a value of something like 4 or more.
However, you will likely need to open the .dds file (if you don't have an art tool that does this, paint.net is a free alternative that can open and save .dds files just fine.) Then you whip out the old eraser tool and just remove these manually.
And since you mentioned it, not sure if you care about this but your wall has some bad UV's, see attached.
