Easy way to close mesh?

Hi, i hope im following all the rules.
My question is, lets say you have been slapping in shapes and not properly building a solid object, eg putting a bunsh of hemispheres on a cube, it all intersects but now you need to build mesh geometry to get it all one skin, is there a way to merge it ? Here is the exact mesh id like it done with

Intersect tool +remove doubles: https://www.youtube.com/watch?v=-rwvxusuJXU

Damn thats bleak. opted to throwing into zbrush and just solidifying it