Evaluation of microfluidic device and sensor designs using continuum modeling is a valuable method, but becomes more complex if nanoscale or molecular level physics must be included in the model. Recently, we have undertaken an effort to incorporate and understand nanoscale effects and how they impact continuum level simulations of microfluidics devices. This research focuses on developing nanoscale simulation methods, and how nanoscale physics can be incorporated into continuum level simulations. The applications currently focus on microcantilevers and biomolecular motors. The main challenge in these applications is the coupling of information generated in nanoscale simulations to the continuum level.