In this thesis I describe the development of a low temperature scanning tunneling microscope system (LTSTM) and its application to the study of charge density waves and vortex dynamics. All the measurements are taken on different 2H-NbSe2 samples with or without impurities to examine the interesting coexistence of the charge density wave (CDW) phase and superconductive phase in the sample at 4.2 K. After creating a structural defect using a voltage pulse, we observed a new type of CDW in the vicinity of the defect. With a Sqrt(13) &times Sqrt(13) reconstruction, the new CDW differs in many ways from the naturally occurring 3 &times 3 CDW in 2H-NbSe2. This suggests a possible local phase transition induced by the tip-sample interaction. As a low-T_c type II superconductor, 2H-NbSe2 is also well-known for the formation of a vortex phase in magnetic fields. Although it was intensely studied for decades, many questions concerning the vortex system still remain unanswered. One of the most important and intriguing questions is the response of the system to a driving force well below the critical value f_c¬. Due to an unexpected defect in our magnet, we are able to utilize a slowly decaying magnetic field with a rate at 5 nT/s to observe the dynamic creep motion of the vortex system which can be described as a Bragg glass. I will also present a study of the statics of this glass phase and demonstrate the use of LTSTM as a powerful imaging technique in the area of vortex physics.