I tried to replace it the publicmap folder but it doesn't seems to work. I guess I have to do some XML but I don't know where to start. Can someone help me out?

Create a new folder in your mod folder named 'PrivateMaps' and in your mod's ini set AllowPublicMaps = 0. Look at BtS' Final Frontier mod if you want to see an example.

If you do that the normal public maps won't be shown, the only maps to chose from will be the ones in your PirvateMaps folder.