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If I upload a document to LSAC in the "final" MS Word form, can Ad Coms open the final and view the file with markup? I was under the impression it simply uploaded the text, not the actual file, but can anyone speak to this? Do I need to make sure each is clear under final with markup view as well?

I don't know what you mean by markup, but the law schools see you applications as they are in the PDF that you have to click on before you can submit.