Hi Nico,
We coudl easily do this on our UP printer at BioCurious. ABS only - doesn't work terribly well with PLA. Sudo Room next to CCL has 3D printers too, as well as a laser cutter.
I'm not quite sure I understand what effect you are trying to achieve. Do you want to print a circular insert that will sit on the bottom of the Petri dish, embedded under the agar? Or are you trying to mold the top surface of the agar, so slime molds will follow the patterns left by the mold in the agar?
If you're trying to texture the top of the agar, mold release may be an issue, but you can probably figure out some mold release agent that doesn't disturb growth of your plants or slime molds too much (vegetable oil?). Alternatives to a 3D printed pattern could include a laser cut one, or even a vinyl cut stencil that you float on top of the hot agar and then peel off to leave a shallow imprint.
Sounds like a fun project!
Patrik