During the Production of BlackRock*Shooter they used Autodesk  3D software as well as digital 2D  animation and combined them together to create the intended Animation .

It seem the rough guideline of the Storyboards were used to guide a rough Blocked 3D version of what was intended , from observation alone it looks like the 3D was then polished to near the final version , the 2D was added on top of it then A software like Adobe After effects or similar was used to add the final polish and effects that were needed .