My first thought is silicone rubber that can be moulded in almost any shape. Silicone rubber may leach chemicals that interfere with your extraction. PDMS may be a material for your experiment.

I think all cell culture insert manufacturers or manufacturers adhering membranes to plastics use similar adhesion methods because they are designed for cell culturing. If the housing is a polystyrene and the membrane is a type of polyethylene, regenerated cellulose, PES, there will be issues In keeping the membrane adhered even though the housing and membranes are fairly resistant to ethanol at 78 C in your time frame.  For example,  tangential flow filtration cassettes aren't cleaned with a hot organic solvent.  Is there a requirement for diffusion through the membrane and a need for high throughput screening?  Not knowing the details of your experiment makes it difficult to suggest an alternative.  But one alternative format may be rapid muliti-sample dialysis systems that have a broad range in solvent compatability specs. One example might be casting you hydrogel (using a syringe) into a sub-milliliter size Slide-a-Lyzer of appropriate molecule weight and then immersion into hot ethanol. This device has a silicon gasket that sandwiches the membrane and may be more resistant. You could the cut out the dialysis "window".

Hello Mariana,

My suggestion is little different. May I ask you that why are you preparing hydrogel in cell culture inserts directly?

According to my experience hydrogels can be easily poured into inserts and they polymerise to take the shape of the cast and they work very fine and not getting any contamination. When you will boil cell culture inserts  at above suggested temperature with ethanol then definitely something is gonna leach out. 

I will suggest to make hydrogel in your standard containers and then pour it in inserts.

Hope it helps !