Materials can be applied to items in the scene by dragging and dropping the material onto:
If you drag the material from an archive, it will appear in the palette where it can be edited and saved with the scene, if necessary.
Presenter uses Autodesk Navisworks selection resolution to decide which items to apply the material to when dragging from an archive or palette into the main view. When hovering over any item in the main view, the proposed selection will change into the selection color (blue by default). When you drop the material onto the current selection, it will be applied to all the items selected. If you drop the material onto an item that is not currently selected, it will be applied to just that item. See Set Selection Resolution for more information on selection resolution.
You can also apply materials to items by selecting the items in the Selection Tree or Scene View, right-clicking the material in the palette, and clicking Apply to Selected Items.
Rules can also be used to apply materials to items automatically based on their layer or color or selection set names, for example. See Use Presenter Rules for more information on this.
You can remove materials assigned to geometry items, either from the Presenter window, or directly in the Scene View or Selection Tree.
Layers can have colors, just as geometry can. If a layer has a material, all its children in the Selection Tree inherit this material, until one of the children is assigned its own material, at which point, all its children in the Selection Tree inherit this material, and so on.
You can drag and drop materials onto layers. Only the layer picks up the material, and although its children inherit the material, they do not have it explicitly assigned to them.
Therefore, right-clicking such a child will not allow you to remove the material because one was not explicitly assigned in the first place.
However, if you use a rule to assign a material to a certain color, then all objects in the scene will get this material explicitly assigned to them, including parent layers and child objects. If, with a selection resolution of something like Geometry (which is more specific than a resolution of Layer), you right-click a child object, and click Remove Materials on the context menu, then the material will be removed from the child object, but not from the parent layer and there won’t be any apparent difference.
To remove the material, you will, therefore, have to remove it from the parent object; in the above situation this would be the layer.