I'm not sure you can do this without using something like java. Scrollbars are a function of the browser rather than the html document itself.
If I have understood your requirements correctly I would use framesets rather than tables to approach this problem. Frames, like tables, can have visible or invisible borders which can be either fixed in position or be moveable by the user.
The contents of each frame are actually separate html documents, thus you avoid the need to duplicate the layout for your header and footer. You can have scrollbars visible or invisible for individual frames which sounds like it would suit your situation.
You need a parent page which contains the frameset, and then a separate html page for the contents of each frame. If I start going into code here I'll make it look at lot more complicated than it is. Just do a quick google search for html tutorials, I found
which seems to cover everything I could tell you here.
The difference between this and what you are suggesting is that with frames the header will always sit at the top of the window and the footer will always sit at the bottom. If your header and footer are large this then limits the available screen space for your actual page.
Most if not all browsers released in the past 5 years will support frames so there should be no compatibility issues unless you are targetting users with very dated systems.
I hope this helps,
tyger.