How to clean outdoor traps?

Solution 1:

If you have weather enabled and your region permits it, rain will clean any tile it touches.

Likewise, you can get your dwarves to move bodies and the like (and if you're playing dwarf fortress properly, there will be a lot of bodies) through the orders screen, and then refuse. There should be an option of "dwarves grab corpses from outside" change that to "yes", and keep "ignore vermin" on if you wish.

Finally, if you have downloaded an updated version of DFHack, the Dwarf Fortress memory utility, you can instantly clean all contaminants from the map by running DFClean.

Solution 2:

Likely the most exciting solution would be to pump water and then lava into the trap area filling it with obsidian which you could then mine out.