How Intersect 3D works
Intersect 3D compares multipatch features and generates new multipatch features based on their geometric intersection. Input multipatch features should be closed. You can check whether multipatch features are closed using the Is Closed 3D geoprocessing tool. If a multipatch feature is not closed, it will simply be skipped and an error message displayed. The tool compares the first set of input multipatch features against the second set, finding all intersecting volumes and writing them as multipatch features in a new feature class. Note that a single multipatch feature in one set can intersect multiple multipatch features in the other. So you might have multiple overlapping multipatch features in the resulting feature class. Because intersecting multipatch features is computationally intensive, care should be taken when selecting appropriate input datasets. For example, if you were to intersect a contaminant plume with multipatch buildings for a city, where the building dataset contained thousands of buildings, the tool would run slowly. If you created a subset of the buildings first that contained only buildings within 50 meters of the plume, performance would be exponentially increased.