is this a watermark or something?

where are those tiles? what is your map size and can you make a screenshot because normally you should be able to change every tile inside the map size.
and which scmdraft version do you have? scmdraft 2 v.0.8.0?

a letter e?

latest version.

they're doodads.

lol you were right!

actually you change the terrain below the doodads (which you will never see and which has no effect ingame below the doodad).

you need to open the doodad window, select a doodad, so that you could place it, then you deselect it and select the ones on your map and hit the delete button on your keyboard.

If you want them to be affected by terrain, just select the doodad, right click, and go to "Convert to Terrain", note that if they're a doodad that uses a sprite, and terrain, that the sprite will still remain, even when you do this.