just paint it out with your surrounding color - whether trim or wall tone. You could add "trim" to the face of the wall and then "cap" the sill / ledge and drill a hole where that needs to push through - the thickness of the ledge trim around it will help hide it.

I'm dealing witht the same issue. Have you found a solution to these bolts protruding up? I am thinking about just cutting them down. I know they are code to secure the framing to the foundation to help against strong winds and tornados. But I have looked in several homes in my neighborhood and others with finished basements and haven't seen a bolt sticking through..

Technically, the bolt should not be there. That is just a window sill, not part of the braced wall panel, other than they used the same board all the way through. A braced wall panel some/sill plate has to have structural sheathing connecting it to the wall studs. This is caused by the foundation crew not looking at the plan, and just putting bolts every six feet. To be done correctly, there also needs to be bolts at the end of every length/board of sole/sill plate, and within 12" of every window that sits down at the foundation level.

The builder should have used a rotohammer, retrofit bolts, and epoxy to put the bolts where they belong. The window sill will just flex/bend before that keeps the wall from lifting.

The window is generally shimmed up 1/4", as should the 3/4" trim board you should use. The nut sticks up about 5/8", which means the trim board should be 3/8" higher than the nut. Tighten the nut again, and then cut off the extra bolt sticking up. Then use a Forstner bit to recess the bolt into the trim board just like blind cabinet hinges are done.