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I am using ArcMap 10.3.

I have this polygon which contains information about different types of soil. I want to clip it, so that only the area inside the other polygon (black border) will be in the output. 2 polygons However, when I use the clip tool, this is the output: There is large areas that have not been implementet in the output file, even though it is inside the clip polygon. There is also an area in the lower right corner that is outside of the clip polygon that is in the output file. Output of clipping And if I use the intersect, this is the output (the clip output is over the intersect layer, showing the difference): The intersect tool managed to get some more areas in the output, but also here, some areas outside of the polygon are inside the output file. Intersect

I used only standard options when performing these tasks, but it seems like ArcMap has troubles with some of the polygons.

Any ideas of what I am doing wrong?

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1  
Shapefiles sometimes contain invalid geometries and are not processed correctly by analysis tools. Does this issue also occur if you first convert your shapefile to a gdb feature class? – GISGe Jan 7 at 10:49
    
That was a good suggestion, as I have had some troubles that have been solved by converting datasets to gdb. However, none of this worked when I tried it now. It gave me the exact same result as output. – 2013US10 Jan 7 at 11:20
up vote 6 down vote accepted

Your shapefile probably contains invalid geometries, there seems to be 'inside lines' within the polygons that are not clipped correctly:

enter image description here

If converting your shapefile to a feature class is not enough, try to find and solve these invalid geometries using the Check Geometry and the Repair Geometry tools.

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I found an error in the clip polygon thanks to the "Check Geometry", and therefore I see why I get the wrong output. – 2013US10 Jan 7 at 12:34
    
Great that you thought of checking the clip polygon too, for me the error was obviously in your soil dataset :) – GISGe Jan 7 at 12:37

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