Metabolic engineering aims at modifying the network of biochemical reactions in an organism to optimize one or more process parameters, such as concentration of a compound of interest (e.g. butanol), robust growth (related to productivity), maximal yield from feedstock, etc. As such, it has been a useful framework for improving production of existing biofuels and for developing new ones. In this discussion, we will introduce different feedstock and biofuel options, and we will describe past, present, and (possible) future efforts for achieving efficient transformation processes. We will focus on genetic engineering (and maybe synthetic biology) approaches, but some issues of overall bioprocess design will be discussed.