Why does it do this to my top layer!

If you want a colored piece on top of another (say a logo) it’s still a bit more tricky. You can follow the steps above and export as a step file, but you will need to split the parts to objects and they will all be laying on the bed. To avoid that you need to make your top piece contact the bed by creating an assembly with a part modifier on the bed (a single layer is enough) then move the top pieces to the desired height. The slicer will show a warning because he thinks the object is floating but your top layer will be clean.

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