Prevention is absolutely the best and most humane way to deal with invasive animals.
Trim back trees that are close to the home
Fill any holes in the home where light escapes
Keep pet food and garbage in sealed containers
Keep storage areas clean
There are also natural sprays that can be used around points of entry. PETAs recipe is oil, horseradish and lots of cayenne. Ammonia-soaked cotton balls are also good repellants for most rodents. If its too late for prevention, its nice to know that many companies offer humane pest removal.
In most cases, the solution involves physically collecting the animals, then doing a thorough cleaning to get rid of the, yep, poop. Trapping wild animals can be dangerous, and there may be babies hidden somewhere. Because the trapped animals have to be relocated, its usually best to call an expert. Organizations like the The Humane Society of America offer suggestions for hiring wildlife control companies. Hiring the right service will ensure that the critters will be dealt with in the most humane way possible.