Mice got into my cabin air filter, how deep I actually clean it all out?

Noticed the ac was smelling off and took out the glove- compartment door and the filter had all mice shit in it. Threw it out, and ordered a new one. But I cannot figure out how they got in, and how do I clean the intake fan (the cylinder chamber where the filter slots)? Car is a 2015 Mazda 6.