Move unused Assets to a specific Folder
I found the solution: The moveFiles function provide the function to move a file:

/**
* Move or rename files.
*
* @param        $fileIds
* @param        $folderId
* @param string $filename If this is a rename operation or not.
* @param array  $actions  Actions to take in case of a conflict.
*
* @throws Exception
* @return bool|AssetOperationResponseModel
*/

public function moveFiles($fileIds, $folderId, $filename = '', $actions = array())


So for me the following code works to move the file with the id 21 to the folder with the id 3: 

craft()-&gt;assets-&gt;moveFiles([21], 3,'', "keepBoth");