RTF is a global modification that replaces all towns in the game.

Don't use an eraser; instead, cut out pixels and paste them onto the base with the correct transparency, for example. You can use empty icons that are stored somewhere in the data.pak as a base. Or you can create one yourself – in Paint.NET, inverting pixels with white transparency successfully creates black, for example. In general, there are several ways. And you can check the color of pixels as usual, using the eyedropper tool.