In Ion Microtomography (IMT), material densities are determined from the energy lost by ions as they pass through a specimen. For fine-scale measurements with micron-size beams, mechanical stability and precision of motion can impact the quality of the reconstruction. We describe several preprocessing procedures used to minimize imperfect specimen manipulation, including adjustment of the center of mass motion in sinograms and correction for vertical translations. In addition, the amount of noise in the reconstruction is reduced by utilizing median (as opposed to mean) ion energy loss values for density determinations. Furthermore, particular portions of the sampled image can be enhanced with minimal degradation of spatial resolution by a judicial choice of spatial filter in the reconstruction algorithm. The benefits and limitations of these preprocessing techniques are discussed.