So Don, that works for sure. Now the issue is that names of my files are kind of random. Some start with the journal title, some with the author, some with a combination. For example, one file may be named "Jarvinen EU 2009.pdf," some are named like "Single+Postoperative+Instillation+of+Gemcitabine+ in+Patients+with+Non-muscle-invasive+Transitional+Cell+Carcinoma+of+the+Bladde r%3A+A+Randomised%2C+Double-blind%2C+Placebo-controlled+Phase+III+Multicentre+Study.pdf."
So while I can add all of the articles (even in batch form) to the Books folder, to drag them into their own collections would be prohibitively onerous. It seems like a software issue. Does anyone know of any other organizing software that would suit my need? Calibre is close, but does not let me make a Collection within a Collection...