First of all, if he's still alive, remove your patch from his entry point(s).  Maybe he'll find his way out.  (Or "her," as the case may be.)  You must be SURE that all animals are out before you do any patching.  Besides, when you do this you'll force him to search for another exit and that puts you, your wiring, and the security of your house at risk. BUT HE'S DEAD AND I CAN SMELL HIM At that point, you have several options, depending on where he died.  Naturally, if you know that, (or you can see him) just pull him out of there (use gloves) and put him in a garbage bag and get him out in the trash. You don't know where he is?  Uh-oh.  That's a problem.  If it's a squirrel, and he's in your attic, he's probably over close to the bottom roof line, where you won't be able to get to him.  Sometimes you can use a rake to get him out.  You might have to dig around in the insulation, they'll use that to make a nest.  The insulation material won't irritate their skin like it does ours, they love the stuff. If he's actually inside a wall or something your options are more expensive.  Naturally, if you know just where he is, open the wall and pull him out.  Wallboard is easy to fix, just cut a hole with a razor knife, (save the "hole") a good wallboard guy can fix it easily if you can't.  As you can imagine, this can get more expensive the more walls you have to open... BUT THE SMELL? Well, there isn't a whole lot you can do about that.  "Deodorizers" don't really eliminate the smell.  They just try and cover it up.  Mostly unsuccessfully.  I really have no confidence in them and I've tried them all.  The smell is just the bacterial action of decaying organic debris. If it's in the attic, and you have an attic fan, turn the fan on, leave it on 24/7 and that will put some negative air pressure to help exhaust the smell to the outside.  Or you can rig up a box fan at your gable vent to help with the job.  You can also use a box fan in the window of a room with a problem of this kind.  You can use both at the same time. WHAT HAPPENS AS THE ANIMAL DECOMPOSES? What normally happens is that flies find the carcass, generally within a few minutes of it's death, and lay their eggs on the body.  The eggs mature and develop into larvae, (maggots) which consume the animal and then crawl away and pupate.  In a few more days you'll probably experience a scourge of adult flies flying around, the ones that have taken care of the dead body.  Not a whole lot you can do about the flies, either....  This generally lasts but a few days, just keep the fly swatter handy.   Once the animal is fully decomposed, that's it.  No more smell.  Of course the skeleton (and other parts) will still be there, like the mummified rat we found in a wall. HOW LONG DOES THIS TAKE? Another tough question.  Depends on how many are there.  And how much they weigh. If you have multiple animals it will take longer.  And the ambient temperature makes a big difference too.  The smell isn't harmful, and as bad as it smells, it will go away eventually.