Does where I do my DIY post-bacc matter?

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Does not matter. Prestige effect is marginal, really, in this case. What matters most are just your grades and whether they came from an accredited 4 year program. I would be a bit wary of whether the med schools you're interested in applying to accept community college credits, but that's about it.
 
n=1 here, but I actually took every science prereq at my local community college and had a successful application season. I knew from the beginning however that I had to ace these classes and do as well on the MCAT as I could in order to overcome any questions about my knowledge base, but it's definitely possible.
 
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Due to a job relocation (I MUST work while doing my postbacc, there is no other way around it - gotta support a family), I am now faced with two options to finish out my DIY post-bacc. I'll be explicit:

1. Harvard Extension School - I would not be formally enrolled in the premed postbacc program, since I've finished most of the basic sciences. I just need a few upper division bios and physics II (ugh, pesky physics).

2. UMass Boston - same, I would just be a nondegree student.

My job position would require me to work 3 days a week on evening shift (3-11). 2 days a week on day shift (7-3). Taking classes at HES is a little tougher but doable, as most of their classes meets 1-2 a week, and UMass Boston's classes are both during the day and evening.

The other options in the area are not possible because:
  • Tufts postbac - not for folks who have already taken most of the basic sciences
  • BU - most of their courses meet multiple times a week in the evening (MET college), or are ridiculously overpriced (day courses as a nondegree)
  • Wellesley - a little out of the way due to not having a car
  • Brandeis, Northeastern - requires formal acceptance into the postbac program
  • and I honestly can't think of any others that are well known
So here's the question: does the prestige of these DIY post-bacc courses matter?

My basic sciences were done at a community college + an R3 state school in Texas (e.g. not the most impressive). I wanted to do some upper division courses to show I could handle more rigorous coursework/get that GPA up. Obviously HES has that "prestige" factor going for it, but it's going to be much more difficult to coordinate times to ensure that my classes fall on the days I need off. Meanwhile, UMass's courses are offered at varying times and allow some flexibility.

Cost is the same for both programs (~$1750/3cr).
I am confident I can get similar grades no matter where I go.
No, prestige doesn't matter...just do well.