I'm working with ArcGIS 10.1, and I have used a polygon with gaps (holes) inside it. Extract by mask gives an improper output with removing the horizontal section of the image where those holes are located ( As shown)



  • Welcome to GIS SE. As a new user, please take the Tour, to better understand how things work here. Please edit your question to embed the images in the question itself. Not everyone (read: very few) will follow links to external sites, so your purpose in posting them will not be realized. Also the purpose of GIS SE is to preserve questions for posterity, which cannot be assured with non-SE sourced images. – Vince Sep 20 '16 at 14:07
  • You should check the topology of your shapefile, since an improperly wound polygon could produce the results you report. – Vince Sep 20 '16 at 14:09
  • Please edit your question to add the images directly to your post rather than providing external links. – Aaron Sep 20 '16 at 14:26

You could try to convert your polygon to raster. Best way is set up the same cell size as the other raster and snap raster in Environments. Then you can try Extract by mask again, but instead of polygon, you will use this raster.

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