You can use Acetone to remove the paintfill.  I've used Testors model enamel paint before to paint using a toothpick and then wiping away with acetone on paper towel once it's dry.

That said I wasn't even close how my Custom Shop putter turned out!  The paint job they did was simply awesome!

I have never done it to my Scotty Cameron putters but I have replaced the paint fill on my irons and wedges quite often.  Currently, I replaced the default black of my AP2"s to be filled with orange paint and my vokey's now sport a combination of orange and royal blue.  It's quite simple to do and doesn't take too long.  The most time consuming part is getting the old paint out, ,but with a little practice you'll get very good at it.

Here's a link with great step by step instructions and plenty of photos

http://www.golfwrx.com/forums/topic/430009-paint-fill-101/

Good Luck!!!

Thanks for the info. I will give it a try and post pics when I am done. 

Nail polish works great but with experience the nail polish markers work much better... the thiner the nail polish the better as it won't get stuck where you don't want it but you will just need to add more coats. Qtips and tooth picks work well to get the paint off. Just be very careful if your putter has a deep mill. My brother spent the longest time trying to get unwanted yellow paint out of the head because it got stuck in the deep milling and didn't wipe off easy where as my old putter was easily wiped clean. To get the previous paint off, you can use nail polish remover but it does take longer than you would think. Youtube probably has some great videos... hope i helped

Here's my putter

Good looking stick! I've always used nail polish and paint pens.  

Drew Angus