I use the tiny rotary cutter to take out tiny stitches and big ones too. Once I can get to where the layers can be separated a bit and I can see the stitches holding the layers together, I pull up the top layer and start cutting with the rotary cutter little by little while continuing to pull up on the top layer and holding down the bottom one. Does that make any sense whatsoever? I have become a master at this technique .... which is a sad statement about my sewing/quilting. Good luck and take your time.
I'd be scared to death that I would cut thru something important, but this sounds like a great technique. Will have to try it on my practice fmq sandwiches.