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I have a QGIS layer with information about administrative boundaries at sub-municipality level. I want to extract only land area in each sub-municipality using information from another layer. I've followed the suggestions here: How to create a new layer from overlap between two layers?.

Each row in the "administrative division" layer attribute table corresponds to one sub-municipality, and each row in the "land area" layer attribute table corresponds to one municipality (for some reason municipality data covers only land area, while sub-municipality data also includes water).

When I use the intersect tool, the created new layer only covers some parts of the layer (i.e., some municipalities, as displayed in picture below*). The pink/purple part is exactly the result I want, but I want it for the entire layer. What is the problem? I've ensured that all rows are selected in both layers.

This is my first time working with GIS-data, so forgive me if it's a stupid question.

**Data privacy note: I've edited the picture so these are not the true administrative boundaries.*

enter image description here

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    Welcome to GIS:SE @SofiaS! Is the CRS the same for your input layers and your projection? Also, it shouldn't be necessary to select all rows as the intersect tool should do this by default unless you check the option to use only selected features. – Joseph Nov 12 '15 at 15:24
  • Thanks for your reply! The two layers were previously displayed in RT90 and SWEREF 99, respectively. I changed both of them to WGS84 and saved those as new files before adding them to this particular project. The project as such is also in the WGS84 projection. Does this give any more of a clue? Regarding selection of rows - I've tried both to select all and to not select at all, but I always get the result showed in the picture above. – Sofia S Nov 13 '15 at 9:12
  • Would you be able to share your data publicly so that others could test it? You can always edit/delete most of the attributes if you want to maintain anonymity. – Joseph Nov 13 '15 at 10:33
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Some things you may want to look into:

  • check the geometry to make sure there are no errors in your vector layer (Vector -> Geometry Validation-> Check Geometry Validation). Sometimes intersect won't work on parts of the layer that have errors. If there are only a few geometry errors, you could go ahead and fix them
  • Try Union. (Vector -> Geoprocessing Tools -> Union). This sometimes works instead of Intersect in QGIS.

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