Using accurate ab initio calculations of the interaction forces, we employ a quantum mechanical description of the collisional state-changing processes that occur in a cold ion trap with He as a buffer gas. We generate the corresponding inelastic rates for rotational transitions involving three simple molecular anions OH−(1Σ), MgH−(1Σ), and C2H−(1Σ) colliding with the helium atoms of the trap. We show that the rotational constants of these molecular anions are such that within the low-temperature regimes of a cold ion trap (up to about 50 K), a different proportion of molecular states are significantly populated when loading helium as a buffer gas in the trap. By varying the trap operating conditions, population equilibrium at the relevant range of temperatures is reached within different time scales. In the modeling of the photodetachment experiments, we analyze the effects of varying the chosen values for photodetachment rates as well as the laser photon fluxes. Additionally, the changing of the collision dynamics under different buffer gas densities is examined and the best operating conditions, for the different anions, for yielding higher populations of specific rotational states within the ion traps are extracted. The present modeling thus illustrates possible preparation of the trap conditions for carrying out more efficiently state-selected experiments with the trapped anions