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

Instead of erasing with a rubber, cut out pixels and insert them onto the base with the correct transparency, for example.
As a base, there were empty icons somewhere in the data.pak, you can use them. 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 check the color of the pixels as usual, with the eyedropper tool.