All media in a specific collection can be retrieved like this:
// will return media instances for all files in the images collection
// will returns media instance for all files in the downloads collection
A collection can have any name you want. If you don't specify a name, the file will be added to a collection named default.
You can clear out a specific collection by passing the name to clearMediaCollection:
Also, there is a clearMediaCollectionExcept method which can be useful if you want to remove only few or some selected media in a collection. It accepts the collection name as the first argument and the media instance or collection of media instances which should not be removed as the second argument:
$newsItem->clearMediaCollectionExcept('images', $newsItem->getFirstMedia()); // This will remove all associated media in the 'images' collection except the first media