Optical design and analysis software codes usually have built-in capabilities for performing rapid tolerance studies on optical systems. However, these built-in capabilities often work on only a few selected performance metrics, such as RMS spot size, MTF, or RMS wavefront error. To tolerance an optical system with other performance metrics, such as ensquared energy, often requires using different techniques. A common method used is Monte Carlo tolerancing. Monte Carlo tolerancing has advantages and disadvantages as compared to using the tolerancing methods built-in to commercial optics codes. This paper discusses many of these advantages and disadvantages.