Array Modifyer, intersecting meshes, and 3D printing

Hi, I’d like to know how to better create single manifold objects from the Array Modifyer. Say I take a dozen cubes and sync them to an empty object, then rotate the empty until the real cubes create a ring of overlapping cubes. If I apply the modifyer I may have one object, but the edges are sloppy and intersecting. Is there a good way to turn this into a single manifold surface for 3d printing? The unnecessary edges make overly complex tool paths.

Solved: netfab basic.