I'm afraid you are wrong. "Außer" is either a conjunction or a preposition used in the way of 'exept for/apart from//besides/save ...
You are looking for an equivalent for the verb 'to save'. In the context provided it is "speichern", "abspeichern" (literally: to store) or "sichern" in German. "Speichern" is used for instance when you save a download on your computer while "sichern" is rather used referring to save files while editing them. "Abspeichern" implies that you have to browse for a certain directory when saving a file or a download.
Please note, this is a general rule of thumb. There are large overlapping areas of both usage and meaning of these terms.
Thus your sentence (or rather fragment of a sentence) would be:
eine pdf-Datei speichern - to save a pdf file
den Inhalt einer pdf-Datei speichern - to save pdf content (referring to a single file)
den Inhalt von pdf-Dateien speichern - to save pdf content (when referring to several files)