Hello, I´m also having the same problem (ERROR 999999: Error executing function. Invalid Topology [Topoengine error.] Failed to execute (Intersect)) while trying to intersect a 5,000,000-point feature with a 2,000,000-polygon feature. Based on the discussion above I guess the only way is to break the datasets into smaller parts? I am a new user of ArcGIS and I am not very familiar with the software. I´m using ArcGIS 10.1 on Windows 7, 64 Bit, 16 Gb RAM. Both files are in a Geodatabase.
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