I understand online PDFs are prone to malware.
Do you have a reference (or some background) for this statement?
As discussed in this question, a PDF certainly can be made to include malware, but I am not sure they are any more prone to malware than other file formats, e.g. flash, or Word/Excel/etc. Or
.js, or other files you find online.
A big question here too is where your files come from: if they are from users, then you have the generic issue of dealing with arbitrary file uploads (see e.g. Should text files or image files be virus scanned during upload?).
If you are generating these PDFs yourself, then I would instead ensure that users can verify the integrity of what they download, for example by making a checksum available, and possibly by using GPG signatures.
I think the answers to your questions would require you to give a bit more background about your situation, and if possible, some idea of what risks you are specifically trying to guard against.