TJ, I've removed the window sections from the cars and soaked them in "Super Clean" or the equivalent until the paint just lifted off. Painted the car, put the decals on, overcoated them, then put the windows back in and put the car back together. After the soaking, I just washed them in soapy water and let dry.
Ted_Roy, a couple of questions....

What are you removing the lettering from and are you going to repaint the entire model?
If the latter is to be answered yes, I might share my amateur techniques that work quite well on standard Bachmann products. (haven't done any of the new Spectrum models yet.)
I've just read K's fabulous article in the Feb 2008 explaining the makeover of the 4-4-0. It's a great, wonderfully detailed explanation of the process. My techniques are much more crude but work very well for me and the resulted end product. The qualifying words here are "work well for me". While the 10 foot rule may be a bit "crude", I do like my makeovers to look good even close up in bright sunlight even though I'm certainly not nor have been "a rivet counter".

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When I paint a Bachmann boxcar, I will remove the roof, the roof walkways, the brake wheel, undercarriage with trucks and grabrails. Then I gently sand the edges and surface of the lettering with 1200 wet dry sand paper to scuff them up. After that, I'll take a mixture of acetone and denatured alcohol dipped in an old Tee shirt and rub over the sanded lettering. The denatured alcohol cuts the acetone into a workable solution and won't allow the acetone to damage the plastic. I do work quickly, keeping watch on the process. I do not remove the lettering completely because of the planking. On the smooth sided stuff, it's much easier.
The next step is to prime the car. I generally prime the car with Krylon Ultra Flat Black. It is a great hiding color, applies without runs and drip, dries quickly and is ready to overcoat in a matter of minutes. If the car is to be painted with a light color, (yellow, gray, or........) I'll follow the black with Kylon flat gray or white primer, allowed to dry for 1-15 minutes and then apply my final Kyrlon color. The local ACE Hardware carries a great assortment of Krylon colors. Again, not being a rivet counter, a close color is good enough for me. /DesktopModules/NTForums/themes/mls/emoticons/blush.gif
The finish coat is usually a "glossy" or smooth finish so when that coat in dry, (after about an hour) I can reletter the car with decals, let them dry for 24 hours and overcoat them with Krylon Acrylic Satin followed by Matte. Put all the stuff back on the car and run it.
Like Henry Ford, my favorite color is black. When the ALPS goes out and I can no longer print white and light colored lettering, I'll have to change my mind...
There is a very important technique for rattle can painting. It's very easy to get a smooth, even coating but it's hard to explain in words. If you're interested, email me so I can send you my phone # and we can chat if you'd like. I can 'splain it better than I can write it... /DesktopModules/NTForums/themes/mls/emoticons/ermm.gif Or come to one of the clinics at the National Convention in Phoenix in May where I'll be doing two on repainting and relettering.
Anyway, this may be more information than you ever needed but this works simply for me.