I would recommend providing much more information than you supplied for this question. Usually all of the 3d operations will fail if you do not have closed multipatches. I would recommend the Is Closed 3d tool and then the Enclose Multipatch tool prior to running the tool again.
"Some 3D set operators are fairly process intensive and may take longer to execute. For example, Difference 3D and Intersect 3D require iterating through every feature in one input feature class, once for each feature in the second input feature class. Each iteration involves determining whether two features overlap, then computing their geometric intersection and writing a new unique feature. As a result, care should be taken when deciding what feature classes to use as inputs to these tools, regarding size and complexity of data."
Generally people use these tools to take simple shapes and make more complex outputs, rather than throwing very complex 3d objects into it to create even more complex shapes.
