You can remove the libraries.
Open windows explorer. Right click the documents library or other libraries and choose delete. You must delete/remove the libraries first before deleting the actual files under C\users\*username*
The downloads folder you can remove from favorites but I do not recommended deleting it. Internet explorer by default goes to that folder, however you can change that in internet explorer settings as well.
Alternatively, you can also hide the folders if you do not want them. Right click the folder-properties. Check the hidden box and click OK. Windows will hide the folder.
Main question-Why? There is really no benefit to doing this, and may cause problems.