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The layer being used as the Clip Features has been used before and worked fine, so I assume the issue is the layer I am trying to Clip (Input Features) - I keep receiving the same error when running the Clip tool :

Error999999: Error executing Function Invalid Topology [Topoengine Error]

The Clip tool has worked fine prior to this. After reading online similar queries regarding this error, the solution in the majority of cases was to change the Input Features to a shapefile - I have done this but receive the same error.

What is my best workaround for this issue?

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Very often these errors are a result of projection issues. –  Aaron May 17 '13 at 16:36

3 Answers 3

Couple of suggestions:

  1. Run Check Geometry tool on your layer that you wish to clip, you could then follow that up with a Repair Geometry if it finds errors. You may wish to do that on a backed up copy.
  2. Check whether the coordinate systems are different. Perhaps you are trying to Clip a dataset in Decimal Degrees with a dataset that is in Meters or vice versa? If so, reproject the Decimal Degrees data into the coordinate system of the other.
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Same Problem, using ArcGIS Desktop 10.2.2. (In case clipping big and irregullar shape)

Solution :

  1. Try to split into small part then clip it one by one, and yes it will take a lot of time and work, but it works.

or

  1. Try to clip it using QGIS (I use QGIS Desktop 2.6), I use QGIS and no need to split it one by one. just select area to clip using definition querry and clip.

I recommended try solution number 2.

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ArcGIS often throws a topoengine error when it runs out of memory while running in 32 bit mode and performing overlay operations. To get around that I either chop-up the job or use 64 bit geoprocessing with lots of RAM and Repair Geometry on all input features (create local copies first if you don't want to mess up your inputs with the repair).

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