Website hacked

In Google analytics i see 11/12 active users in my website, pointing to urls that don’t exist anymore. Those pages were injected with some kind of virus. I deleted all the folders and malicious scripts from the database, but those pages are still active with the 404 error and still indexed on search engine.
I tried to exclude the urls with the google removal tool but it’s the same as before. I don’t know what to do now. There are more than 24.000 fake urls indexed that lead to nothing and active users, Bots i think, that try to visit those pages.

The page I need help with: [log in to see the link]