How to clean up after those %#*&#@ squirrels?  That's a tough question.... It kinda depends on how sensitive you are. And how long they've been in there. And how "dirty" it is.   If they've been there a long time, and if it's REAL dirty, or if you just want to be anal about the whole thing, you would clean up the poop, (most will come up with a dust pan) and then you could spray the area(s) with one of those enzyme sprays, you can get it at local pet supply stores, or your local animal groomer might have some. DON'T spend a lot of money, I have heard that it sometimes doesn't work that well. (DON'T use a bleach mixture, and DON'T EVER MIX BLEACH WITH AMMONIA! Let it dry well before you assess if you need to reapply.  Then, wet it down with plain water from a Windex-type bottle and see if you still get the smell - be fussy.  Re-apply, if you think you need to re-apply. After all that, if you prefer, you could PAINT the those same areas with an alkyd-based primer. If the insulation is permeated with droppings, (and you're being anal) you could replace the insulation. It is extremely difficult to remove the poop from insulation. You're better off removing and replacing, if you're going to do it at all. The squirrels will use several places to "use the bathroom." After awhile, this can be many places and you may notice a distinct odor of urine, again it will depend on your own sensibilities. The paint will help to cover future odors, make sure you use several coats. If the squirrels have made rub marks on your siding, try to remove those by cleaning and/or painting. Squirrels have a pretty good sense of smell and they are programmed to follow other squirrel's scent trails. They LOOK for this. Depending on how dirty those areas are, you may also want to use a respirator. If you do use one, use one that is qualified to remove solvents, not just a simple dust mask. You can get good throw-aways for about $25 from your local paint store. Make sure it will do the job or don't use one at all. One that is insufficient is virtually useless. If you can't find one, we have the correct one for sale at our OnLine store for less than $28, no shipping charges.  Just go here and scroll down to respirators. A final question? Is a respirator necessary? Depends. There are jobs where I have not used one. If you catch them before they are in too long, it will make for amuch easier job, if you really have to do it. That said, there are plenty of structures that AREN'T cleaned up and don't seem to have a problem. When I do squirrel jobs, I don't normally include any cleaning, and in most cases, I don't think it's really needed unless the structure has been inhabited for years.