Measuring the level of a ubiquitous RNA in just four cells labelled with GFP

I have a stack of images through a fly brain. The brain has been hybridized with a Alexa 647 labelled probe against a mRNA which is fairly ubiquitously expressed. I’m interested in the level of this RNA in just four closely spaced cells which I have labelled with GFP. I would like to use the GFP to segment the GFP expressing cells away from the non GFP expressing cells to enable me to measure the levels of mRNA in the GFP expressing cells without interference from the non GFP expressing cells. This would be easy in 2D even for a non programmer like me but how would I do it in 3D? Thank you.