Yes, and no!
If by "late model duke" you mean a 998S or 998R (both of which came with a bellypan) then the answer is no for a couple of reasons. Firstly, you would have to cut off the part of your side panels that return under the bike and secondly, the little vents at the bottom of your sides are completely different to the vents on a 998 and hence the 998 belly pan will not align properly with your side panels (assuming you'd already trimmed the return sections off).
However, there are several options for fitting a bellypan to your bike. There are loads of companies that can supply a race bellypan but again you would need to "trim" your side panels to fit. Your best option would be to buy two new GRP race side panels and a carbon bellypan. If you go to somewhere like
Vimori, their side panels can come in either Ducati red or yellow (not painted but part of the manufacturing process and a really good colour match) and they will also do you a carbon bellypan. Pretty decent fit as well. Vimori used to supply D&E Racing with all the bodywork for their 748RS race bikes. Side panels are approx £65 each and a carbon bellypan is approx £150.
Personally I think that would be your best bet. The last thing you want to do is chop up your perfect original side panels just to fit a bellypan.
Oh yeah, and the belly pan as fitted to the 998S & R is really just a "looks" thing. It isn't fully enclosed at the bottom and is nowhere near as deep as a full race version. Compare a picture of one of the factory race bikes against a stock 998S or R and you'll see what I mean.
This topic has been covered before so do a search on "bellypan" for other opinions, info, etc etc.
Hope this helps!
Neil
P.S. If you want any more info feel free to drop me a line.