Photodissociation of mass-selected populations of trapped ions is used as a tool to determine the spatial distributions of the ion clouds under a variety of trapping conditions. These ion tomography experiments are performed in both the axial and radial dimensions, and the results show that the ion cloud expands significantly in the radial dimension as the number of trapped ions is increased. This expansion correlates with an increasing error in mass assignment due to delayed ion ejection. Furthermore, both effects appear to be related to the occurrence of compound-dependent (rather than mass/charge ratio-dependent) effects on ion ejection. The molecular ions of nitrobenzene and n-butylbenzene, and the benzoyl cation, examined under fixed conditions using the same number of ions, each displays different mass shifts which correlate with differences in the magnitudes of their radial distributions. These results demonstrate that the spatial distribution of a collection of ions depends on their physicochemical properties. Furthermore, alterations in the geometry of the trap are shown to be a means of controlling the compound-dependent positional distributions as well as the corresponding mass shifts. Ion tomography measurements of the size of the ion clouds are made for all three types of ions as a function of the number of trapped ions. They show that the compound-dependent mass shifts can be eliminated by symmetrically increasing the spacing of the end cap electrodes, a procedure which deliberately increases the positive octapolar field component. The implications of these results for exact mass measurements using ion traps are considered.