Coupling femtosecond pulses to the scanning tunneling microscope (STM) has the potential to combine unprecedented spatial and temporal resolution. Although much progress has been made, there are significant challenges that lie ahead. In this talk, I will highlight our efforts in studying the interactions between laser pulses and single molecules in the STM nanogap junction. I will also discuss the directions we are headed in to further our understanding of molecular dynamics using laser pulses. Challenges, successes and failures will be presented.