For starters, dwarves currently won't clean:
- Soil layers
- Above ground areas
- Constructed walls
You can remove contaminants from a wall by removing the wall. (Note: I don't recommend doing this.) The building material will be contaminated when it comes out. The miner or builder who removes the wall will 100% certainly be contaminated if not wearing gloves. This miner or builder will also very likely be contaminated even if fully dressed, because they have to come in close contact with the contaminated area to do their job, and close contact is the definition of plague spreading in DF.
Whether or not this miner or builder contracts the plague himself, the next bathtub this miner or builder goes through will get plague in the water. Bathtubs are high priority for cleaners when engraved--but the cleaners can't just teleport there instantly, or finish the job instantly. (You could station janitors in the tub, but they will just tend to wind up standing in plague, and come down with it, before they decide to start cleaning. I learned from experience.) Injured dwarves who may have dropped a boot and move through the tub, such as to the hospital, will be infected. (Example: A goblin bit your foot off in the execution room. Now you've got the plague because of that miner who decontaminated the wall! It happened.)
Anyone who hauls the contaminated building material away will also contaminate the first tub they go through. The building material will get clean from that, but your shoeless dwarves won't thank you.
Clearly this is a nightmare. Plague that can survive on surfaces indefinitely is a nightmare. It's hard to find and it's hard to clean up (if it even can be cleaned-up). You don't want it. But you have it. What to do?
There is one solution that definitely works. This substance has to be located and sealed off--and it has to be sealed off while standing in a tile that is not contaminated. If you can prevent the builder from getting contaminated and avoid creating contaminated building materials, then nobody will get sick from this contaminated tile (once it's sealed). But how?!
First, you have to do everything in your power to keep dwarves from continuing to step on or next to the contaminated areas while the builders work:
- Identify contaminated areas and deny access to that section of the fortress, such as via a burrow.
- I mark contaminated areas as Restricted Traffic so that dwarves (and invaders, who can likewise spread contaminants) will do everything in their power not to step there. Traffic designations will also help you keep track of places that have been contaminated and sealed off in the soil layers (where contaminants are not visible), so that you don't try to do anything else there.
Hopefully, nobody will starve or dehydrate while your builders save the fortress. This is why it's good to have multiple stockpiles of food and beer, and clean water sources throughout the fortress. At Nutscaves, before proper quarantine measures were in place, the dwarves had to be sealed off from each of the three vital things at various times of plague.
So, next we must build a wall all around the contaminated area, and a floor over the top of it (if the top isn't already sealed). Why a floor over the top of it? Because if you don't, mark my words, some unlucky dwarf or animal will find a way to fall inside there someday. (It'll be so much !!fun!! getting him out without contaminating the fortress...that's coming from one who knows!)
Make sure the builders will not have to walk through the contaminated areas to get to the materials they'll use, or to build the seal itself. You can control the direction the dwarves build from, by designating a statue to be built in the tiles you don't want (can't let!) them to stand in, and suspend the construction of the statue. So, suspend statue construction over every contaminated tile and adjacent tiles, before doing anything else. I always keep some junky statues around the fortress for this simple purpose (and others).
This is painstaking, nitpicking work especially in soil layers where contaminants are invisible in the GUI, but it's worth not getting any dwarves sick. The last of the very worst strain of plague in my fortress is, as far as I know, currently entombed by stone walls and floors next to the trade depot. No one has had it for seven years. (We currently only have a weaker blood plague and the light necrotic plague active, that I know of, and I haven't been able to track them down. I suspect they're on pieces of clothing somewhere...it's time for another fiery sacrifice of our worldly goods.)
Now, as long as we never tear down those walls and floors entombing the plague (or find an object that magically survived with contaminant on it), we should never get that particular plague again.