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Check out this quick mod I made, that cuts the base off to make it flat and printable:
https://www.thingiverse.com/thing:1511957

Or if you use the original file, see if your slicer has an option to skip the first 1mm and use that (In Cura go to Advanced -> Cut off object bottom -> set to 1.0)

He set the STL file at a position of -1.0mm in the Z axis, but most slicers that I know of ignore the position of the object and will print the whole object.

Wireframe Skull Pencil Holder (Flat base)