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Ok, Michelangelo is starting to get a few on his shell, so I know you use a toothbrush to gently brush them off. Do you use anything else?

Also it looks like his shell is getting ready to shed, should I be extra careful so I don't pull off the scutes?

I'll probably be doing this in the next week or two as I plan on cleaning the tank during spring break. (since it takes so long) And I figured I'd clean him up when the water was clean too. That way everyone is clean for a while.

I don't think anything else is really necessary. The scutes should come off when they're ready, so I'd just handle him normally (but gently).

If you have hard water with a lot of minerals, the deposits will eventually return.

Yeah I know they will return I just gotta brush him. But I haven't changed the water in a while so this is the first time I've seen deposits on him and that's what they are I checked to make sure it wasn't shell rot or anything else. Gently with him is like saying pet the porcupine but don't get pricked. He moves too much but I'll keep him in a small container to try and restrain him without hurting him or having to hold him that way it'll be easier on the both fo us, especially since he loves to fight anything I do with him.

I like your analogy to the porcupine lol. My RES hates to have his shell wiped down, which I do periodically. He's a lot bigger than Mikey, but I usually get a grip from underneath on his plastron, and although he'll struggle for a while, there usually comes a point where he stops and just looks at me as if to say, "OK, you win. Get it over with." Then I have that small window of opportunity before he decides to start up again...