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Are you using a directory tool to get the list of files that are then fed into a dynamic input?
If this is the case, you could create subdirectory number logic by counting the number of slashes in the file path, and then filter out files with a level count above whatever threshold that you specify.
The directory tool would still take the processing time to identify the file names, but you could limit the number of files that were actually read in by filtering out the files that aren't relevant.