The final step in cleaning up a scene is to visually inspect the Outliner, Hyperhshade and Hypergraph for any objects that aren’t needed and weren’t cleaned in any previous step yet.
The objects are often linger because they are objects with shaders applied. Because Maya can’t tell which objects you intend to use and which you have forgotten to delete, these objects still remain.
How to Look for Lingering Objects
In Wireframe Mode make sure you have the Move tool selected. You can then begin selecting objects and determine where and what they are in the scene. If you can verify that any are unnecessary or have been forgotten then delete accordingly.
Name everything in your scene, don’t let your file get cluttered with default named objects. This will help keep scenes clear of forgotten objects. In the Hypergraph you can see grouped objects and stray objects possibly not intended to keep.
How to Delete these Nodes
Hypershade > Edit > Delete Unused Nodes Will delete any nodes in the Hypershade that are linked to an object. Do this step after you have gone through the Outliner.
In the Hypergraph Be Thorough follow these steps to clean up unused nodes.
Show Input/Output Connections –>
Show assigned shaders in Hypershade –>
Select all nodes in the connection stream in both Hypershade and Hypergraph This includes the ShadingGroup node –>