I cut it full and running. I took a piece of 1/4" clear acrylic the same width as the brace and cut it the full length as the brace. Most people cut the center brace, leaving an inch or two on each end to attach the acrylic to. Then they place the acrylic piece on top of the tabs on each end and glue or screw it in place.
Since my tank was full I didn't want to chance cutting the factory brace, so I took the acrylic piece and placed it on top of the old brace and drilled two holes on each end for the plastic screws and nuts I bought at Lowes. Then I put a drop of gorilla glue on it and put it under the old brace and put the screws though the holes I already drilled and tightened them down. I let it set up over night, then cut the old brace off an inch or so past the screws, leaving the clear brace underneath.