Tech Shop (a Bay Area maker space for artists and entrepreneurs)
Ace Monster Toys - Hacker space in Emeryville
Campus:
The College of Environmental Design has a
shop with 3d printers
and workshops.
There are more of these printers in the
Soda/Etcheverry Hall area. I'm not sure to what extent any of these are open.
See also commercial options:
Shapeways Molecule Models
Here is a nice description of how to use open source software to make the input files.
The link above describes how to make a VRML file on the way to the final format. There are many VRML generators for Chemistry some of which are nicely described at the National Cancer Institute.