A system and method for using near-infrared or short-wave infrared (SWIR) light sources for identification of counterfeit drugs may perform spectroscopy using a super-continuum laser to provide detection in a non-contact and non-destructive manner at stand-off or remote distances with minimal sample preparation. Also, near-infrared or SWIR light may penetrate through plastic containers and packaging, permitting on-line inspection and rapid scanning. The near-infrared or SWIR spectroscopy may also be used to detect illicit drugs and their chemical composition. Moreover, the spectroscopic techniques may also be applied to quality assessment and control in pharmaceutical manufacturing, thus permitting the implementation of smart manufacturing with feedback control. Fiber super-continuum lasers may emit light in the near-infrared or SWIR between approximately 1.4-1.8 microns, 2-2.5 microns, 1.4-2.4 microns, 1-1.8 microns. In particular embodiments, the detection system may be a dispersive spectrometer, a Fourier transform infrared spectrometer, or a hyper-spectral imaging detector or camera.