If layer not need, you can remove them.
Exists two ways for remove the layer:
1) Inside layer toolbox, select target layer and simply press to "remove" button. Layer will be removed, but member items will be moved into default layer.
Delete layer and Keep items menu item
2) Inside layer toolbox, press to target layer by right mouse button, and you can remove layer by item menu, also you can remove member items from map with layer (Inside SMBX, layer always removing with member items).
Layer context menu
Layer "Bricks" was removed, layer "Water" - is hidden
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