PDF is a read-only format that is not meant to be edited. A lot of times the PDF files are too complex to be properly converted to another format. Our conversion software does the best job it can, but some PDF's converted to another document/ebook format just won't turn out perfectly. You can try to convert the PDF into a .txt file for a plain-text file, then convert that to your output type.
If you have no need to edit the file after conversion, you could convert the PDF to an image format (like JPG), then to your desired output format.