Find some snap in plugs at a local true value. Then if you ever want a windshield again you won't be re drilling.

Or some small stainless carriage bolts?

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So I want to fill the small holes on the to deck where the wind screen/shield used to be. Is there anything I can use that will be easy to color match. The plan is NOT to paint the boat for a while. I don't want a bunch of colored spots though. Any ideas?

Without pics it's hard BUT, if they're just small holes.......how about you just dab some resin/hardener in each with a toothpick and level the holes off.   Then go to Home Depot or Lowes paint departments and try to find a color (those little color cards our wives like to grab) and find one that comes close to matching.

Once you have one that comes close to matching, take it to the autobody supply store and have them match it in a small sample of paint.    Take that and with a small brush, dab each of those spots you filled and wait till it dries and then buff/wax it and run it that way till you're ready to do the complete paint job.

Just a thought............john

im a fan of filling the hole first rather than just slapping some gelcoat over the top.  so i drill em clean, get a dowel, or in home depot they have a whole section of round wood in various sizes and fill the hole along with some resin to hold it in place.  then take a countersink drill bit and drill the top out a little bit.  like mentioned above west marine has a gelcoat repair kit, its fairly inexpensive with a couple little tubes of tint.  mess around with the tinting until you get it a good match. fill the countersunk hole up and leave a little extra on the top.  once it dries wetsand it down smooth and then take a little bit of rubbing compound to polish the area up and your hole will be nice and filled.