What do you want as far as "clean"? I've tried to recommend items that have relatively little cursing and at least glossed over sex scenes. Some of these have a fair bit of violence though, although I've tried to stay away from ones with graphic violence as much as I can remember.
There are some good fantasy classics that fit this bill:
The Hobbit and The Lord of the Rings by J.R.R. Tolkien
Narnia books by CS Lewis (and his other fiction.)
All of the Discworld books are good and while there is some innuendo there's nothing more than that. Some of these are just candy but many of them have much more to say about modern times than appears on first glance for such a humorous and playful series.
I'd try the City Guard (starting with Guards! Guards!) or Moist Von Lipwig books (starting with Going Postal) from Discworld. Personally, I think a lot of the Witches sub-series is the best but it doesn't cast magic in a "less than bad light". Same with the DEATH sub-series. The City Guard and MVL series pretty much ignore it although it is around.
A more recent series is The Paper Magician series by Charlie Holmberg, although it's YA.
For more science fiction titles:
The Wool Series by Hugh Howey is very good. Some violence but I don't remember it being graphic.
The Murderbot series by Martha Wells (more language and violence in this one but very good.)
The Martian and Project Hail Mary (which just came out) by Andy Weir have some language but not the violence or sex. Two of my favorites.
Brandon Sanderson's books are generally clean;
I'd start with the Mistborn series (or just skip to the Wax and Wayne books - Alloy of Law - unless you are very spoiler prone; these are a sequel series to the Mistborn books. They have a very different feel however.) He also has YA science fiction and super-hero series and a mega series called the Stormlight Archive. The Stormlight Archive is already over 5,000 pages and only the first 4 books have been published, out of 10 planned.
The Hitchhiker's Guide to the Galaxy is fun; there are 5 (or 6?) books in this "trilogy". The often zany humor is not for everyone though.
For something more serious, I really enjoy a lot of Ursula LeGuin's works as well. Some of her works are very accessible (
Earthsea) and others are much deeper (Left Hand of Darkness or The Dispossessed) but I've enjoyed all the ones I've read.
If you are ok with short stories, this is a good one: The Paper Menagerie by Ken Liu
http://io9.com/5958919/read-ken-lius...fantasy-awards