As long as you use an acrylic, enamel, or lacquer paint it's usually easily removable.
I used enamel because from my experience enamel paint and the thinning agent(zippo lighter fluid in my case) were the least destructive. Plus the materials are easy to find at your local arts/hobby store(micheals for me).
My favorite paints to use in modelling is lacquer but lacquer thinner wreaks havoc if you're not careful.
Acrylic is removed by a number of liquids. Windex, rubbing alcohol, and lacquer thinner all work to some degree on acrylic paints.
Here's an example from today of what I used enamel paints for to fill in the black lined vents of this model.
EDIT:
So this is the general idea of how I did my engraving. It's a much larger scale and I didn't use a pre-mix product like the guy in the video but this will pretty show you the process.