Cold, trapped atomic ions have enabled the investigation of fundamental physics and generated a rich field of applications. Foremost among these is quantum computation which has recently driven the development of the sophisticated, scalable surface-electrode trap. Despite the many advantages of surface-electrode traps, the typically smaller ion-electrode distance, d, in these traps results in an increased ion heating rate that is proportional to d^(-4) and a decreased trap well-depth that is proportional to d^(-2). These shortcomings can be simultaneously addressed by installing the trap into a cryogenic environment. With this in mind, a closed-cycle, cryogenic ion trapping apparatus that maintains excellent vacuum, is highly modular, has increased optical access, and uses a simple vibration isolation system has been developed. Single ions are trapped and used to characterize system properties such as the motion of the vibration isolation stage. In order to compare this system to a similar room temperature apparatus, the ion trapping lifetime and heating rate are determined. A single ion also serves as a sensitive electric field probe that is used to measure and compensate stray electric fields across the trap. Due to the long dark ion lifetimes in this system, it is well-suited to probing the stability of small, linear ion crystals. Linear ion crystals of arbitrary length are built in an automated fashion using transport waveforms and the scaling of dark lifetime with ion number for N <= 6 is investigated. These data are then used to consider the relevance of various loss channels.