Files exist, but Finder only sees Aliases

This morning I was looking for a file and noticed that my Documents and Movies folders were completely empty in the Finder. If I search for a file that is in one of those folders, it will come up in the results but clicking on it from the search gives this error: "The alias "example.jpg" can't be opened because the original item can't be found." It gives me an option to Fix Alias but that never allows me to actually click on anything.

The thing is, if I am using a program to search for files, they will still exist and can be opened. For example, if I click File > Open in Photoshop, I can go to Documents and see example.jpg (and all the rest of the contents that should be in Documents) and I can even open it without a problem.

I have searched online and most people seem to have a problem where their files are replaced with aliases, but that isn't my problem; my Finder simply can't see those files and Search thinks they are all Aliases.