Whether you have create your website design layouts with the help of HTML tables or CSS, in both option you can make your website search engine friendly if you actually design it in proper manner by arranging all designing elements.
With CSS based layout it is easy to do any changes in design because if you wants to do any change you have to change CSS only one time and changes has been automatically done in all pages whereas in table base website design if you wants to change anything you have to makes changes in all individual tables.
Check this video explained by Matt Cutts http://www.youtube.com/watch?v=fL_GZwoC2uQ