In a linear Paul trap, atomic and molecular ions can be trapped and cooled by a method called laser cooling to so low temperatures that the trapped ions form an ordered lattice - an ion crystal. In this project I investigated how to control chemical reactions between trapped ions and a background gas, as well as methods to purify ion crystals and control their shape. Finally we used the purified ion crystals to investigate optical pumping as a continuous quantum Zeno effect and compared the results to theoretical models and calculations.