How Difference 3D works
Difference 3D compares multipatch features from two feature classes and subtracts all overlapping areas from one of them. The 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 multipatch feature in the first input feature class, called the minuend, against every multipatch feature in the second multipatch feature class, called the subtrahend. If it finds an overlapping volume between any features in the first and any features in the second, it subtracts that overlap from the minuend feature. It does this for every feature in the minuend feature class. Note that some of these features may be completely removed from the output if they are completely overlapped by a feature in the subtrahend feature class. Because this comparison and calculation can be very time consuming, care should be taken when selecting appropriate input datasets.