A portable spectral imaging microscope includes a probe head coupled via fiber optic cabling to a laser source and to a spectrograph. The probe head is coupled to a position controller that is mounted on a base suitable for positioning adjacent to a sample. The position controller has five degrees of freedom that permits one to adjust the position and direction of the probe head relative to the sample over a wide range of dimensions and angles. The entire probe head can be easily moved in order to precisely align the objective lens to stationary samples for simultaneous viewing and spectral analysis.