I think it depends on the material used for printing the parts, we ordered the FED3 housing from Shapeways printed on PA12, once I emailed them about the recommended solution to clean this material, and they said it is okay to use soapy water!
We do not put the FEDs inside the cage, rather we have them mounted outside the cage, so the parts of the FED that are exposed to the mice (the nose poke and the pellet well) become seriously dirty over time, I follow this procedure:
1) Use a compressed air duster to remove dust and debris( I recommend putting on a face mask).
2) Use paper (wet wipes) and soapy water to clean the body (it is better to spray it on the paper rather than on the FED to avoid accidentally damaging the electronics)
3)Use q-tips (already sprayed with soapy water) to clean the edges that are not accessible via paper or wipes.
4)Finally, before moving the FEDs to the animal facility, we use 70% ethanol to disinfect the FEDs which also helps to clean them. (again you can use paper or q-tips or wipes)
(if you are using superglue to adhere the nose piece, make sure the solution you are using won't dissolve the glue!- so to have better control, it is better to use q-tips once cleaning that part of the FED)