Layer refers to a game concept, that a map can have two layers: the surface and the underground. Every map has the surface layer, but can also have a second, underground layer in it. The map-maker must decide at the beginning of the map creation whether to make it an one layer or two layer map.
Heroes can move from layer to another through Subterranean Gates, Monoliths, Whirlpools, or by Town Portal. There may be nothing visual that distinguishes the surface from the underground. However, all combats that take place on the underground layer are battled as they were on Subterranean terrain.