Is there a simple process in ArcMap v10.2 that will allow me to overlay three raster images, whereby any obscured pixels will be deleted in the output file?

I do not want to retain the values of any pixels that are being covered by upper layers, because any overlapping pixels will alter future statistics that I run to determine count.

This is how I envision my final raster:

enter image description here

The bottom layer is a supervised land cover classification raster that has been smoothed over with a 7 x 7 focal statistic (comprised of five classes), which is meant to be my "base" layer. The middle and top layers are both reclassified images of the bottom layer, and have been smoothed over with a finer focal statistic to retain some detail.

All of these rasters are the same extent and pixel size -- based on Landsat 8 imagery.

Apparently, I am looking for some sort of unweighted overlay tool that simultaneously removes underlying pixels but I have not been able to find this capability in the Toolbox. I have already tried using the Merge tool, Combine tool, and Mosaic To New Raster tool.


After playing around with the advice given in the comments, I believe using the Con expression as part of an equation in the Raster Calculator would yield the best results. I would like to build an expression that states "if the value of [middle layer] is 2 then keep [middle layer's] values, but if the value of [middle layer] is not 2 then use [bottom layer's] values." Then I would perform a similar calculation to stack the top layer over the combined bottom and middle layers. If there is a way to stack all three layers using one equation, that would be preferred.

  • Do you have access to a spatial analyst license? Any of the really in-depth tools with rasters need this license. If you do not you will have to consider GDAL_Calc or QGIS Raster Calculator for this operation. From your picture Cell Statistics should do it resources.arcgis.com/en/help/main/10.1/index.html#//… if you set your NoData cells to Max data value then use the MINIMUM operator. More complex operations can be done with Con resources.arcgis.com/en/help/main/10.1/index.html#//… Apr 19, 2015 at 23:01
  • 1
    2 mosaics operation will do the job.
    – FelixIP
    Apr 20, 2015 at 5:35
  • Hi @MichaelMiles-Stimson -- I do have a license for Spatial Analyst, but I think most of the tools associated with it are more comprehensive than I need. Could you please elaborate more on your suggestions to use Cell Statistics or the Con tool, though? Seems to me that Cell Statistics MUST perform some sort of weighted analysis on the pixels (I wish there was just an option to choose "visible" or something along the lines of that), so I believe the Con tool might work best. Do you know which layers I would use for the different variables, particularly the Input conditional raster? Apr 20, 2015 at 17:44
  • Hi @FelixIP -- See my response to Mr. Che's answer below...I just want to be able to slap these three layers together and export only the pixels that are visible. Apr 20, 2015 at 18:07
  • If you have Spatial Analyst license use Raster Calculator help.arcgis.com/en/arcgisdesktop/10.0/help/index.html#//… with the Con operator. I would need to know the logic to help expand to a conditional statement e.g. If R1 is Null then R2 else MinOf R1,R2. A simple set of rules in pesudocode (human speak) would help.. please edit question with details and I'll get back later. Apr 20, 2015 at 21:42

2 Answers 2


You could try mosaicing:

  1. Add every of your rasters to mosaic (top layers should be first).
  2. Set Mosaic Operator to First.
  3. Set Nodata value.
  4. Save mosaic as tif file.

enter image description here


If you have changed your raster's symbology type to "classified" and want to overlay this images, then you can use Reclassify tool before mosaicing.

  • Hi @MrChe -- Regrettably, your suggestion does not seem to work for my purposes. I think that because I've formatted my imagery so that it's displayed by classes/intervals instead of bands, that may be why I can't use the Mosaic tool. Apr 20, 2015 at 18:03
  • See update in the answer. Apr 21, 2015 at 4:44
  • Looks like the Raster Calculator is going to work out fine for my purposes, @MrChe, but I'm going to keep this in mind in case it doesn't. I'll also admit that I was trying to use the Mosaic tool before realizing that I needed to create a Mosaic dataset first, which is likely part of the reason why it wasn't working for me. Rookie mistake... Apr 22, 2015 at 18:57

Thanks to everyone for all of the help!

I was able to create an equation in the Raster Calculator (using the Con expression) that stacks my layers and keeps only the visible pixel values. Here is the two-part method that I used:

  1. Ran first calculation to stack middle layer (R2) on top of bottom layer (R3)

Con("R2" == 2,"R2","R3")

  1. Ran second calculation to stack top layer (R1) onto the combined middle/bottom layer (R4)

Con("R1" == 1,"R1","R4")

  • Con("R1" == 1,"R1",Con("R2" == 2,"R2","R3"))? the expressions can be stacked like Excel expressions... via an intermediate (R4) works, if you're happy with that then so am I. Apr 28, 2015 at 21:18
  • Oh, I see. Wish I could test it out (I don't have access to ArcMap right now), but I understand the logic. Thanks! May 14, 2015 at 15:46

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