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I was trying to export features from multiple layers in a common region into new shapefiles after selecting them using the "Selection By Polygon" tool/button. However, the "Selection by Polygon" tool only selects features from the top/current layer (QGIS 3/2.99 as of July 2017).

Is there a way to select features from multiple layers (e.g. all visible layers or all layers) by drawing only one polygon?

I don't want to draw the query polygon for the region several times as it is tedious and the polygons I draw could be slightly different each time.

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    If you have selected some features in the layer you want to Save as..., the Save only selected features option supposed to be active (thats how it works in previous versions), so it could be a bug. – Oto Kaláb Jul 23 '17 at 10:29
  • @OtoKaláb Thanks, you're right. There were multiple layers, and the Select by Polygon tool only affected one of the layers. The layer which I tried to export had no selected features. I've edited the question for the new problem. – laser Jul 23 '17 at 12:44
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You probably don't have any selection in layer you want to export.

If you have selected some features in the layer you want to Save as..., the Save only selected features option supposed to be active.

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