QuarryPlus has frame mode, which digs inside the frame.
Use 4 markers and right click quarryplus before sending energy.
See the pictures below.

1. How to place markers.
   
   
2. Right click quarryplus to change its mode to Frame Mode.
   
3. Worikng
   
4. Work has done.
   

Use quarryplus to flatten your world. (Other machines don't have this mode.)

Okay so I can use frame mode to dig holes in walls then?

I think you can do it.
Notice that you can't remove bedrock and other unbreakable blocks because ChunkDestroyer doesn't have frame mode.

I won't implement it because it can make your save file too big. In normal world (default world creating), there is no bedrock or unbreakable block that stops quarry's horizontal mode work. It means quarry can't stop and load world infinitely.

Oh. Yeah I didn't think about that part.

Right, but what I mean is, in 'horizontal mode' like I was suggesting, the quarry would act like a tunnel bore and dig indefinitely in a straight pattern. Frame mode is cool for making holes, but I mean like just an indefinite non-stop hole going in a straight direction kind of like how it works in normal mode until it hits bedrock.