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If you decide to have the fairing mirrors removed, the best way to fill the holes is to start from behind the inner fairing. Either epoxy something to cover the holes or use fiberglass mat and resin. You want to have the holes covered first. From the front you will have the holes but they won't be trough-holes. Then you would use a standard body filler to actually fill in the holes. Make sure to feather edge the filler out past the circumference of the holes otherwise you could end up with the filler popping out. I've never seen a stock inner fairing but for some reason I thought they were textured. If so, the texture can be replicated using a number of different methods depending on the texture pattern. You would want to texture the body filler as it's drying.
7 Surprising Harley-Davidson Products that Are Not Motorcycles
Slideshow: The bar-and-shield logo shows up on far more than motorcycles, some of the company's most unexpected products have nothing to do with riding.
Slideshow: From the troubled AMF years to modern misfires, these bikes earned reputations for reliability issues, questionable engineering, or disappointing performance.
Crazy Bunderbike Build Looks Amazing, But Is It Impossible to Ride?
Slideshow: The Swiss custom shop has taken a Harley Softail and stretched it into something so long and low that it looks closer to a rolling sculpture than a conventional motorcycle.
Engraved Rebellion: Inside Bundnerbike's Glam Rock II
Slideshow: A standard cruiser becomes an intricate metal canvas in the hands of a Swiss custom house known for pushing Harley-Davidson platforms far beyond their factory brief.
Slideshow: Harley-Davidson's challenges aren't abstract; they show up in dropping shipments, shrinking dealer traffic, and strategic decisions that aren't yet translating into growth.