If your professor uses a Mac, consider Devonthink by DevonTechnologies.
http://www.devon-technologies.com/products/devonthink/index.html
For searching, the software has an artificial intelligence system, keywords, meta data. It can store PDFs, word docs, emails, notes. It can be integrated with a scanner so you can scan and store documents in the database. It's got OCR built in...
I have DevonThink (personal edition, not Pro/Office) and I don't even use 1/10 of the power built into this system. You should check out some of the reviews online and videos of people using DevonThink.
I'm not saying I think it's a *bad* idea for doctors to think like scientists.... but they don't. (speaking as a scientist who took classes with premeds)
Our current system for picking/grooming future doctors almost always selects for the least scientifically-minded students--science is the opposite of memorization, but the students who memorize the best are the ones who get into the best med schools.
MD-PhDs are very very different from regular MDs.
The hardest part of climbing the ladder of success is getting through the crowd at the bottom.