Perhaps...
setAutofilter returns a Worksheet object, which is unlikely to match what you want, and that is not viewable (except by a var_dump or equivalent).
The cells you want to display are selected by an automatic filter? If so, I advise you to read the documentation (PHPExcel AutoFilter Reference), you will find an example explaining how to apply a filter before saving the file (by default, the filter is applied at this time) and a sample display of filtered cells.
Otherwise... Be more specific in your request.
setAutofilter returns a Worksheet object, which is unlikely to match what you want, and that is not viewable (except by a var_dump or equivalent).
The cells you want to display are selected by an automatic filter? If so, I advise you to read the documentation (PHPExcel AutoFilter Reference), you will find an example explaining how to apply a filter before saving the file (by default, the filter is applied at this time) and a sample display of filtered cells.
Otherwise... Be more specific in your request.