It is a common practice in insulator-based dielectrophoretic separation to use and reuse PDMS-constructed microdevice for an extended period of time while performing biological and technical replicate experiments. This is usually done to rule out any effects of device variation on separation efficiency. Ensuring that all experimental conditions remain the same is critical to the conclusion that can be drawn from such repeated experiments. One important contributing factor to the flow of materials within the device is electro-osmotic velocity, which stems from the surface condition of the device construction materials. In this paper, we present an affordable microwave-based (MESA-Mgen) oxygen plasma cleaner developed for approximately less than $100 using readily obtainable parts from an average local hardware store with no specialized tools. This low-cost room-air microwave plasma generator was designed using an R-4055, 400 W, 2450 MHz half-pint household microwave oven (Sharp (R)) for exploring the possibility of sealing polydimethylsiloxane (PDMS) devices onto glass with minimal budgetary commitment. Microfluidic channels generated using MESA-Mgen were evaluated for their electro-osmotic velocities while factors including contact angles, storage-solvent, half-way hydrophobicity period were also explored with MESA-Mgen, and the results were compared to those obtained from the commercially available plasma cleaner (COM-PC). These outcomes revealed that the MESA-Mgen induced hydrophilicity and ensured leak-free sealing of PDMS substrates in a manner comparable with the COM-PC.