PDMS array on nitrocellulose
Below is an image of the PDMS array on the nitrocellulose membrane. I’m trying to create a stamp that can be applied to the NC membrane, before PDMS is poured on.
The idea is that the stamp will be heavy enough to keep the PDMS from soaking into the areas of the NC that the drug and protein solutions should soak into. The purpose of the PDMS is to keep the solutions from mixing on the NC membrane, because the membrane is very hydrophillic. A problem that I am encountering is that when I add vacuum grease to the already cured PDMS (what I’m currently using as a stamp), the vacuum grease makes the NC more hydrophobic. Does anyone have any ideas of what material I could use to make the stamp for the PDMS array (I was thinking of either using metal or rubber)? How I can get it to keep the PDMS from adhering to the NC in specific spots?

Nice illustrator images. Wow, you are a quick study!
Silicon can be patterned and used as a PDMS mold. It might be easiest to begin with a design for an arrayed membrane and design a complementary mold. Start by chatting with Mike and/or Henry about what they know about mask design.
I’m not sure what you have tried, but getting a stamp to work as you describe it is pretty tough when you have an array of wells. Have you tried making a PDMS film with holes in it, painting uncured PDMS on one side, then applying the NC to the gooey side? You could then throw it in the oven to cure.
If all you are trying to do is isolate regions of the NC membranes, could you just heat-stamp it? You could create an Aluminum stamp, heat it to the softening temperature of NC and hard press it onto the membrane. Seems like you would be able to collapse the pores wherever the stamp is applied, while preserving those areas that you don’t heat/compress. This is similar to how those heat-sealing vacuum packagers work. Just convince Jim to buy a heated press – we need one anyway for future hot-embossing microfluidic work. You could also just build a cheap one with a few parts from Omega, but I’d rather see you buy a big new Carver embossing press.
There are also more exotic techniques using optical patterning of photoactive compounds, but these would likely mess up the NC.