I'm using Acrobat Pro XI
In previous versions I remember being able to mark a section of the document and erase it by simply pressing delete. This allowed me to take a scanned form that was filled out and delete the filled in portions in the various boxes. Either I am completely unable to locate that function or it is not available for some reason. Am I missing something? Any help would be appreciated.
There's no such shortcut in Acrobat. You can use the Redaction tool to remove certain areas of the file, though.
The way you describe, I think you were in Edit PDF option and here you can select different layer. However, in cases of scanned files you may face issues as Acrobat may not recognize text on the document. If that is the case you can try running OCR on the document as then click on Edit to check if that what you are looking for. I may not be correct, I'm just assuming what you are trying to do.