Hi Mathieu I would also recommend trying the FGDB ideas given above. And if Xander Bakker's good looking code doesn't do the trick, I have some further options that might be worthy to check out. We ran into similar problems at work while processing a large number of (raster)data in Python scripts. The following helped us solving similar issues as you are currently experiencing: Monitor your computers memory while the tool runs using Task Manager. Should there be a memory issue, or if the above ideas using the FGDB does not work try the following: Write a .BAT file that accesses the Python.exe and then opens your script. Insert all the necessary arguments in the command line script. You can prepare the batches using an Editor or Excel. This way you'll be able to process a large number of iterations of your script outside the ArcCatalog environment, which (in case there are any in the first place) would solve the memory issues, because running a BAT-script means that the Python environment is closed after each iteration and loaded again for the next. Hope this helps.
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