In QGIS 3.16.10 I want to clip (remove) the polygon areas (yellow) in one layer from a larger polygon in another layer (gray).

I've tried the Clip from the Processing Tool but it only returns the yellow areas, "Only the parts of the features in the Input layer that fall within the polygons of the Overlay layer will be added to the resulting layer", but I want the opposite result (the brown polygon with holes where the yellow polygons are).

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I've also tried the Clipper plugin but can't figure out how to make it work (I'm a novice). I've searched but can only find methods that give the "Clip" result or talk about clipping a raster with a vector polygon. Seems like removing a polygon from another polygon should be easy.


2 Answers 2


Try the "Difference" that will do exactly what you want:

Extracts features from the input layer that don’t fall within the boundaries of the overlay layer.


'Input layer': gray
'Overlay layer': yellow


and get the desired output


  • The description for Difference indicates it is for removing portions of polygons that partially overlap, not when one polygon is completely within another (as is my case). I've found a way to use Clipper that works. I'll write it up.
    – ldekay
    Commented Sep 10, 2021 at 23:32

The Clipper plugin will work, though it's pretty temperamental.

  1. In my case I usually have to merge the layers (then display them rule-based so I can confirm they're all present).
  2. Then I hide the large enclosing polygon in the merged layer and select all the smaller polygons I want to cut out.
  3. Then I run Clipper>Clipper Clip with multiple selection. Finally bulk select the entire polygon(s) and deselect the large encompassing one.
  4. Then bulk Delete the smaller polygons, which leaves holes (windows) through the larger polygon.

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