If you know you want to do biotech, one big part of the PhD is finding a lab that is doing relevant work that industry will find useful. Engineering is a great choice. Any of the biomed PhDs or chemistry based ones could work well if the work is related. You need to see where former graduates head to get a feel for this. If you have any interest in the business/entrepreneurial side of things, I recommend putting out some early feelers with the business school and the tech managment office for the university to see what is out there.
The other big part of it is networking and culture. By this, I mean that you ideally want a PI who is already interfacing with biotech and has contacts and former students you can ultimately leverage for a job or other opportunities. Some great indicators can be a PI who has SBIR or STTR grants, tends to patent and license his/her research, or does a lot of biotech consulting.
Culture matters a lot. You want to be able to make your career goals and interests clear to the PI and have them be very supportive. Most biomed PhD labs are so heavily oriented towards academics that you may not find a supportive culture in the lab or dept for rounding out your education for industry.
That, of course, is an ideal case if you can find all these things in one lab. If not, be proactive about looking carefully through all possible depts. Be upfront and tactful about your goals when you talk to PIs about long term work in their labs.
Also, try and figure out if there are any PhD grads, MD grads, or MD/Phd grads that headed in the general career direction of interest to you. Talk to them early. Odds are they will already be pretty familiar with the layout of the university and have great advice for you.
