You can use multiple sheets in a workbook or multiple layers in an image editor to get a third dimension in existing 2D data editors. I've done some weird things like pack numeric data into RGB pixel values when I needed to annotate an image with a couple bytes of data per pixel in irregularly shaped regions...
If Minecraft is an actually serious possible solution to what you're doing, maybe a world editor for it would be useful? I don't know what's popular now (been OOTL for too many years) but people used to make custom maps in MCEdit; some of the 3D brush tools and such might be useful depending on what you're doing?
Can you provide more details on what you're trying to do?