I am using Raster Calculator in ArcGIS 10.4.1 in order to substract two raster surfaces. However, when I substracted the two surfaces an error 000539 was appeared! I tried to adjust the two surfaces in a specify extent, but clip and extract by mask tools didn't work as I wanted. I tried to fit the first surface into the second one, however, one more column was remained in the former surface. Any suggestion?

  • Make sure that the coordinate system of the environment settings is the same as the input raster coordinate systems
    – BERA
    Apr 4, 2017 at 5:02
  • I set the same coordinate system as my raster layer, and the same error appeared. I transferred the data in QGIS, following the same procedure, and there wasn't any problem Apr 4, 2017 at 8:43

1 Answer 1


A colleague and I just had a similar error with rcexe. Looking at the error, it appeared to actually be a problem with NumPy. After a lot of investigation including looking at the path that the ArcMap python version is using, we realised that the path contained Anaconda. This meant that python was trying to use the NumPy version from Anaconda and not the ArcMap version.

Couldn't work out where the path was being set (as it was not in the windows path), but changing the folder name of the anaconda files fixed the issue.

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