— functions described here could have a different name (I’m using the german version) —
Open the pool, rightclick > remove unused media > “remove or trash?” > trash. Empty trash in the pool.
Safety:
Use the pool function ‘archive files’ before. That way all media gets collected into the project folder. Alternatively you should look through the trash in the pool before deleting it, looking for pathes.
In case you’ve imported files into your project from Media Bay or explorer, they are maybe just referenced (depending on the import settings set in preferences) without actually being imported into your project folder. The ‘empty trash > delete’ function in the pool will relentlessly delete the files. You won’t find them in your OS’ trash, they’ll be gone simply.
Another way is the ‘backup project’ function as mentioned before. If you choose to ‘delete unused files’ in the dialogue, they will not be deleted from the original project, they’re just not taken over to the new folder.
Indeed you have to delete everything you don’t want anymore from the project window. In case you have stacked takes there’s a function called ‘delete overlaps’ (rightclick menu in project). This will remove all hidden stuff underneath the events on top. If you were using track versions there can also be some invisible stuff left. The cure is to select all tracks and use ‘remove track versions of selected tracks’.
It’s easy once you understand how Cubase handles files. I admit it’s not as intuitive as it could be 
The mentioned ‘clean up’ function is to be used very very conscious! I did it just once…