If all you are doing is creating a different architecture without making significant changes to the actual content (so giving each existing page a more SEO friendly category +/or file name) then you just need to make sure that every individual page is correctly redirected to its new URL using 301's. External links will remain in play and search engines will eventually recognize the redirects and update their indexes.
As long as you build the new structure in parallel so that you never take a page out of circulation you should be good.
If, on the other hand, you plan on altering content, removing pages completely, or doing something that will make existing pages unavailable for any period of time, you are likely to see some impact on rankings that might not be ideal.
If your concern stems from the fact that you are maybe not sure whether the new structure will actually help, then you will want to start slowly as Nicholas suggested.
My approach would be to do exactly as Nicholas described, but to start with pages that are ranking poorly.
Happy 301'ing 
