I would suggest to use the Find Advanced feature to find unused items. This way you can identify and clean up unused documents (including entities) from your model.
Go to Edit > Find Advanced (Ctrl+Shift+F) and change the Search for dropdown to Unused items. Now click Find. This will show a list of all unused items.
Using this list you can clean up your project. You might need several iterations of this, because removing a document can cause another document to not being used anymore. You can easily use the Refresh button for this.
It is a best practice to clean up you project once in a while and keep the unused items to a minimum.
Items which are not used doesnt mean that they are REALLY unused. For example, if a Deeplink MF is being used, it wouldnt have any usages but technically it is used. Usually i have a practice of marking such elements as used! which are then picked by the Advanced Search mentioned by Kilian.