Administration of drugs can help in the recovery of the brain for example after a stroke. There are many available delivery routes such as intravenous injection or local injection in the brain. Whereas, the former encounters problems with systemic side effects, the latter requires multiple invasive brain surgery. Local drug administration could be achieved with a drug delivery implant to reduce the amount of invasive procedures and to include useful features such as electrodes for monitoring neural activity. In this study an advancement is made towards spatial control of permeability in a membrane. Porous PDMS membranes were fabricated by replica molding in a 3D-printed mold. The smallest pore diameter was 100 μm and the thinnest membrane thickness was 160 μm. The permeability of such a membrane is tested by a dye which must go through the membrane in order to observe staining in 0.6% agarose gel to simulate diffusion of brain tissue. No staining was detected using pristine PDMS membranes. However, a fast flow from hydrophobic to hydrophilic side was observed in a PDMS membrane recently treated with plasma on a single side. Furthermore, slow diffusion of the dye was present in a less hydrophilic, dextran-modified membrane that received plasma treatment on one side as well. Thus, the permeability was controlled by the wettability of the membrane surface without modification of the entire inner pore. The same experiments were performed on a mouse brain to be compared to the results on agarose gel. The use of agar as a brain phantom material is useful for further investigation of a local drug delivery device, but a few improvements are required to better correspond to the brain.