When loading a menu link tree, you get the entire tree that fits the specified parameters. However, when using that tree, you probably want to perform some checks and remove certain items. A common example is to remove the menu links to which the user doesn't have access. This is where manipulators come into place.
The MenuLinkTree service has a transform() method, which alters a tree based on an array of manipulators. The latter take the form of callables, typically service names with specific methods. So, the actual manipulators are services that traverse the tree and make alterations to the tree items, their order, and so on.