I can't find my icons, but they're there?!?

My computer caught a virus, which I was able to remove by using safe mode and Malwarebytes, but now I can't find any of my desktop icons. At first, I assumed the virus had just removed them, as it had removed my desktop background and wiped my start menu, but when I tried to recreate some of my folders, it said that that folder already exists. I tried to download Minecraft, and put it on the desktop, and it said that was already there too. The thing is, I don't see these icons, my desktop is barren! Please help if you can, I'm confused, and I'd rather not have to rebuild my desktop from scratch if I don't have to!