Berries and dye can be used to paint on various surfaces and structures. With the intended berries or dye, right click on a surface/structure, click paint and choose what color you want to color with (if you have only one type of berry or dye, it'll automatically paint with that color without a popup). With this you can make masterpieces, graffiti, and color with multiple colors on one thing (only one can be used at a time). A screen will pop up with many small tiles and you can choose where to paint. When you click finish after painting on the screen you will have successfully painted.
See also: Berries