A scanning tunneling microscope (STM) was developed to work in conjunction with a Hitachi S-4100 field emission scanning electron microscope (SEM). To achieve the necessary five degrees of freedom for sample and probe movement, an entirely mechanical method was used, employing pairs of parallelogram flexure hinges actuated by set screws driven through gear reduction. The STM was also configured such that the sample is mounted on the piezoelectric scanner and the probe is fixed. This allowed the sample to be positioned close to the objective aperture of the SEM. The role of the SEM was envisioned primarily as an alignment tool to position the STM probe over a region of interest on the sample. The STM would then complement the SEM by revealing different surface detail. The instrument was successfully used this way, to image small structures such as Molecular Beam Epitaxy (MBE) and Metal Oxide Chemical Vapor Deposition (MOCVD) grown GaAs/AlGaAs heterostructures and long gate MOSFETs. It was also used to measure the depth of e-beam fabricated calibration pits. Two methods of STM lithography were investigated. Field evaporation of probe material produced mixed results, due in part to the experiments being done in vacuum. Field evaporation proved a useful method for clearing contamination from the probe. STM probe induced modification of passivated silicon surfaces was also investigated. A voltage threshold for depassivation was found and a model for formation of etch masks at positive polarity was proposed. Patterns were written and successfully transferred to the substrate by wet chemical etch. Lines were as thin as 20 nm, and up to 15 nm high. An important result of the lithography research was the discovery that the SEM could image depassivated regions at low accelerating voltages. This allowed some light to be cast on a number of STM imaging artifacts, as well as allowing precise calibration of imaging range. Artifacts included the effect of a finite tip radius on imaging steps and grooves, imaging on highly contaminated surfaces, multiple tips and dielectric material acquired by the probe near the tunneling junction. The effect of electron beam induced carbon deposition was investigated. The STM was used to measure the depth of thin carbon deposits. A deposition rate of between .6 and 2 nm/sec at 300,000X was found.