Many molecular processes take place in regions of space, time, and/or frequency that are difficult to access experimentally. For instance, visible light microscopy is often limited by sample scattering issues, as well as by the lack of natural fluorescence in many molecules of interest. Complex biological and chemical systems inherently have multiple resonances at a variety of frequencies, such that single-frequency laser excitation rapidly becomes cost-prohibitive. Ultrafast (femtosecond) lasers can, with appropriate pulse-shaping, provide solutions to all of these problems for a wide variety of applications. Sample investigations into molecular ionization dynamics, non-destructive imaging, and chemical identification will be discussed and compared with theory.