How can we properly clean up after a squirrel?

Okay, I've never posted here, but we have a weird situation. We had a very intense storm with extremely high winds. Our neighbors found something in their yard, and thought it came from our house, but when we looked at it, we thought it was just someone's shattered birdhouse. We found out in a bizarre way that it was actually the chimney cap from our house, when we got home one day, to find that our house was completely ransacked. We thought that someone may have broken in, but saw no signs of entry. We looked around, and when I went upstairs, I found a squirrel sitting on our bedroom windowsill.

Now here's our situation. We've been at my parents' house because we need maintenance done at our house that we can't afford right now (in case you're wondering, it's my wife's aunt and father's childhood house that was given to us as a starter home when we got married in 2019.) It took days to get the squirrel out of our house. We trapped him in our office, and he just refused to go in the trap. We finally led him out, but he defecated all over our office. What is the best way to clean up this mess and properly disinfect any surfaces that he may have been on? We are desperately seeking answers. Thank you for your help in advance!