I have two overlapping layers of polygons, and I need to somehow erase the areas the overlaps. -This way i should end up with two layers of non overlapping polygons. Sounds pretty simple but I just can't get it right with any of the tools in Qgis!? Should i use "clip" or "cut shape by polygons", or perhaps the "difference" tool and the "clip"?

Whatever I do the product isn't right.

  • 2
    If you use the Difference tool on layer A and layer B, you should get a resulting layer C that doesn't overlap with layer B (layer C is layer A with the overlapping areas removed). Is that not the result you want?
    – Jake
    Commented Sep 25, 2013 at 14:13
  • Hi Jake. Thanks for the reply. -Well, it's part of the result that i want. The polygons that comes out as the result of the Difference tool is wrong though. It doesn't "Clip" or "Cut" out the small areas that overlaps, instead it removes the whole polygon that is in contact with the other layer and, as i said, not just the "tiny" area that actually inflicts with the other layer. Does the problem makes sense?
    – aneh
    Commented Sep 25, 2013 at 14:24
  • In that case, you should simply reverse the operation (B-A instead of A-B).
    – Jake
    Commented Sep 25, 2013 at 15:12

3 Answers 3


using qgis 2.0.1. created two overlapping polygons (yellow & green). clip tool creates "difference area" (red polygon). apply difference tool; input vector layer = original polygon layer, difference layer = clip polygon.

two arbitrary overlapping polygons

results of applying clip polygon with difference tool to each of the original polygons.

using clip with difference tool on both original input polygons

hope this helps:)

  • I think that there is something wrong with the topology in my layers. When i use the clip function, it doesn't register all the overlaps, only some of them. Could this be the reason for the problems. I realize that when you have the clipped out the overlapping areas, you can use the difference tool, to remove from one of the two layers. Thanks for all the responses! postimg.org/image/5lwq2lwqv/2626db87
    – aneh
    Commented Sep 26, 2013 at 7:25
  • @Andreas I am poking around in the dark on this one, but check the coordinate systems of all layers you are working with, including those created with the difference tool. Perhaps there is a mismatch with projections? I know this can cause issues within ArcMAP
    – Barrett
    Commented Jan 8, 2014 at 14:50

You can also use "symmetrical difference" (vector > geopprocessing tools) to do what you want in one step (also called XOR, see a description of overlay operations on wikigis for more details)

On the other hand, your topology does not seems very good because you have overlapping polygons. You could clean up a bit your green layer by converting your polygons to lines and back again from lines to polygon (vector > geometries)

By the way, before using the processing tools, it is also recommended to work in the same coordinate system. This could explain why your tools are not working as expected

  • the link does not work anymore 'infogeoblog.wordpress.com is no longer available.The authors have deleted this site.'
    – Lennert
    Commented Feb 26, 2018 at 13:16

You can use clip command in Editor to clip overlay polygon, you can see here https://youtu.be/TGg18r5U4yw

  • This does not answer the question. Could you provide an answer using QGIS and not ArcGIS Commented Dec 2, 2016 at 8:10
  • also that youtube video is no longer available
    – csk
    Commented Feb 26, 2018 at 19:33

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