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I have about 12 different land cover shapefiles (all have common attribute data) that I need to select only pieces of it out. After I run the select by location on all 12 shapefiles, is there a way (python, model builder or tool) to batch export all of the selected polygons from all shapefiles out at once instead of exporting them out one at a time?

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If you are exporting into a database, you can right click the database and select import multiple, then select the 12 layers in the drop down. The import should honor your selection

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