You can either knock out or saw a hole through the catalyst core, leaving only the baffles at the outlet side of the OEM muffler/cat. You might try that first - I prefer the tone that gives compared to many of the aftermarket mufflers.
I used a hole saw, driven by the nut that holds the actual saw cup to the mandrel instead of the shaft that normally goes into the drill chuck. Put a deep socket and an extension on the hole saw nut, then drive that with whatever power tool you might have. The hole saw allows you to drill a hole through the core that flows a little better than removing the entire core.