You don't need my tools, although thanks for the recomendations.
Make sure your list of urls is saved. Then go to trim to root and then remove duplicate domains. Export this list and save it, Ill call it list B for examples sake (assuming List A is where you saved your original list of urls).
Then clear that out and load List A into the urls harvested section. Go to import >> select url list to import and compare - then select list B. This will then look at any urls in list B and remove them from the loaded urls (your original list). So that will remove all the root domains and leave you with submdomains.
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