Option 1:  Use Object Styles

Many elements in Revit have the material set as “By Category” by default.  This means that the element will have the material set for its category in “Object Styles”.  However, many categories do not have a material set in Object Styles, which results in the element not having a material, and thus, being ignored by ElumTools.  This is an especially common issue with MEP and Structural elements.  You can change the Category Materials as shown below.

Option 2: Edit the Family.
Open the family up in the Revit family editor.

Each primitive (extrusions, sweeps, etc,) within the family has a parameter to define the material as shown below.  Often, the default material is “By Category”. This means that the category material, as defined in object styles, will be applied (see Option 1 above).

You can also apply materials to individual surfaces using the Revit paint command as shown below.