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enter image description here

I have rasters in each folder and I want to merge rasters of each folder and save them individually. In above model I am able to merge all rasters from both folders. Any way I can fix this in a model builder?

Raster of C1- Will be saved as C1_Merged Raster of C2- Will be saved as C2_Merged

For showing purpose I have made 2 folders, I need to run on 1000 folders.

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You need to read the help file on the subject of embedding models within models. You would have a master model that is iterating over folders (your C1 and C2) and that feeds each folder into a sub-model which would be the model in your sample image. You would pass the folder name into your sub-model using inline variable substitution.

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