Here's what worked for me on a set of 2001 cans, which are probably the same as yours.
Remove cans from bike. Remove the two bolts holding the bracket in place. Get a big piece of wood, hold tightly on the aluminum sleeve and pound the inlet into the wood until the sleeve slides down a ways. It would only slide about three inches for me.
Decide how much you want to shorten the cans. I cut mine by three inches, which leaves the "Ducati" logo on both sides, but just barely. Mark the sleeve at a three inch distance around, then put tape on the cans to mark what you want to keep and to form a straight line to follow. Using a hacksaw or cutting wheel, cut around the sleeve to your desired length.
Next, using a hacksaw, bandsaw, or other cutting device capable of cutting through steel, cut all the way through the inner can about half an inch from the end, just below the end cap. I used about three hacksaw blades doing this.
You might want to reverse the order of the above two steps.
Remove the tip, slide the cut piece of the outer sleeve off, and prepare to make your second cut through the inner can. I cut mine as far down as I could without touching the sleeve with my saw.
You might want to do some cleanup work on the remaining interior part, but I didn't bother.
If you want to paint the outer sleeve, now is the time to do so.
Get some red high temperature slicone Permatex and run a bead around both ends of the outer sleeve. Do the inlet end first, then slide the sleeve into place and bolt the exhaust hanger bracket back into place. Run a bead around the outlet end and pound the end cap back on. Drill at least two holes through the sleeve and into the end cap, then either screw or pop rivet (preferred) the end in place.
Reinstall on your bike and enjoy the new and improved sound.
_________________________________________________My method lets out the Ducati sound but isn't so loud. You can cut it shorter and remove more of the innards if you want.
The best way to cut is if you have a bandsaw available. With other saws, it works much better if you have a helper to hold the can while you cut (or take turns cutting). If you need to clamp the can while cutting, be aware that anything that applies pressure to just two sides will leave dent marks in the aluminum that won't go away (which is one reason I painted mine).
If you don't seal the ends with permatex, you'll have exhaust gasses escaping from the edges at both ends, especially the inlet end. You'll be foreever cleaning them. I ran mine for a couple of weeks, then took them back apart and sealed them.
I did mine last week, basically the same way on http://www.ducatisuite.com/mufflers.html but I used a dremel. I left them the stock length and just removed the steel wool packing and cut the end baffle out. The sound is definately louder and better.