Question: I'm to test a programming idea I have in Blender. I need to combine multiple cubes. I want to create lots of duplicate cubes, and then delete all faces that are doubled. 

I know there is the remove double faces, but that doesn't do what I want. It leaves a single face where two faces were. 

[![Blender two cubes](https://i.stack.imgur.com/NLm2w.png)](https://i.stack.imgur.com/NLm2w.png)
In this example, I want to join the two cubes, but where they join, I want both faces deleted since they can't be seen.

Answer: 
* 'Remove Doubles' (that refers to vertices, actually, not faces) as you already have..
* In the header *Select* menu: *Select All by Trait* > *Interior Faces*
* `X` > *Delete Faces*
To do that, turn on all vertex visibility,

Select all the Vertex at the point of contact, then look for "Loop Tool" under the editing panel in the "Tool Shelf" 

Use either "Bridge" or "Loft" in the "Loop Tool" option.

It will join them together