When mine got scale rot, the edges of her white belly scales became pale brown and ragged. I didn't notice a change in the upper part of her body, but she's a Bloodred and it might just have been a trick of her natural colour. No blisters either. She'd spent too much time in her humid hide (I'd left it in after she shed as she seemed to prefer it). Feedback was that the twin causes would be her being in too damp an environment for too long, and me not changing the substrate in the humid hide often enough. It wasn't filthy - she'd never pooped in it - but the environment was warm and damp, which was the perfect breeding ground for bacteria.
IF yours has scale rot (bear in mind that it's difficult to diagnose anything over the net and without a pic, so see a vet if in any doubt) then you need a very basic hospital setup. Paper towel substrate is good - I used newspaper. You need to use hides that can either be thrown away or easily disinfected. The idea is to do away with any nooks and crannies that bacteria could use as a refuge to multiply.
Change the towels/newspaper every day or every other day, even if she doesn't poop on it. Disinfect the tank and fittings every other day with a reptile-safe disinfectant. Wipe the snake down every day with a disinfectant. This doesn't win you popularity points with the snake I'm afraid!
I had to keep up this regime for a few weeks before I saw an improvement. She was also lethargic and went off her food during this time. She didn't start eating again until she'd gone through a couple of rapid shed cycles to clear off the damaged scales.
I used Betadine for my viv and snake and that did the trick. It was a slow old job though.
Good luck with yours. Hopefully there will be other ideas here soon as well.