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I want to extract the counties (green area) overlaying with another feature class (pink area) using ArcGIS 10.3.1 (Advanced). I am using spatial join and find the Join_Count > 0 to select out the involving counties. Is there a better way to do this process or what are some alternatives?

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You can use "Select by Location" From "Select --> Select by Location" You can then specify if you want to select counties that the pink area to completely contain a county, intersect with it or various other options.

Then you can right click on the counties layer-->Export selection and save it as a new shapefile for future use.

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