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I can't figure out a method or find a tool that would completely delete (or disregard) just the overlapping polygons (red) that intersect with the Puerto Rico polygon (black). I essentially want to create a shapefile with just the polygons that don't intersect with the black polygon. I am using ArcGIS 10.3.

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    I believe you're looking for Erase, though using Union and selecting out the not-NULL black features is also possible (if you don't have an Advanced license). Please take the Tour and be sure to always specify the exact version of software in all questions.
    – Vince
    Feb 11, 2017 at 22:16
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    Do you want to disregard the entire polygon if it intersects PR, or just the intersecting part?
    – phloem
    Feb 11, 2017 at 22:20
  • I want to disregard the entire polygon. I have tried looking into the Erase tool and other common tools with Intersect, but I'm not trying to clip out a certain geometric shape. I just want to remove the spatially overlapping red polygons. I am fairly new to ArcGIS though.
    – user91411
    Feb 11, 2017 at 22:45
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    @user91411 Comments are intended for potential answerers to request additional information or clarification. Your response to these requests should be as an edit to your question, not as a further comment. Please update your question with your additional info.
    – Midavalo ♦
    Feb 11, 2017 at 23:11

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You can remove the overlapping polygons with a Select by Location then Delete.

First use Select by Location, either with the Select Layer by Location tool or from the Selection menu in ArcMap. Select features in your red polygon layer that intersect features in your black polygon layer.

Then Delete - either with the Delete Features tool or Start Editing, and delete selected records.

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