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The way it was modeled might be confusing Slic3r - try some other softwares like Cura or RepG: they all have different ways of dealing with model problems. I encountered a similar problem with my models when I used boolean operations incorrectly in Blender - Slic3r would repeat a bunch of layers just like that Might also be able to fix the model somehow but it can be kind of difficult to see what's wrong.