Clones are specializations of operads forming powerful instruments to describe varieties of algebras wherein repeating variables are allowed in their equations. They allow us in this way to realize and study a large range of algebraic structures. A functorial construction from the category of monoids to the category of clones is introduced. The obtained clones involve words on positive integers where letters are accompanied by elements of a monoid. By considering quotients of these structures, we construct a complete hierarchy of clones involving some families of combinatorial objects. This provides clone realizations of some known and some new special classes of monoids as among others the variety of left-regular bands, bounded semilattices, and regular band monoids.