I think the basics are to use a SurfaceModeller transformer to drape a layer onto a DEM.
From there you could (for example) create a TINSurface. Point the TinSurface into a PointCloudCombiner and it will create a point cloud that can be written to Minecraft. But then I guess that doesn't get you much more than if you just said "write my DEM point cloud".
I guess my question is, are these geological layers just the surface layer (the bedrock that a geological map would show) or are they three dimensional (or layers with depth) that represent multiple strata?
If it's just the bedrock then maybe a different output of the SurfaceModeller would help (DrapedFeatures) or even use a Group-By to create multiple surfaces.
I hope this helps somewhat. I know that Minecraft can "model" different layers which is why I'm wondering if you want to create proper strata, or just the same bedrock all the way down.