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On Qgis 2.16 when I am using the extract nodes command, even when I save to file with a specific name, the result is a layer named "Nodes" with the extracted points. I have to go to the folder where I saved the .shp file and load it in the program. It is not a major problem, it is somehow annoying. Do you have the same experience?

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You have to change the settings under Processing Options -> General to activate Use file names as layer name as you can see below, then it will use the file name as you save it in your directory.

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