To meet the increasing needs for precision products while maintaining a low cost, a systematic tolerance analysis tool for size and geometric tolerance during the design stage of a product is essential. However, despite the importance of tolerance analysis, the development of tolerance analysis methodologies has been stagnant mainly due to the complexity of geometric tolerance. To overcome the difficulty of geometric tolerance analysis, this paper first develops a geometric tolerance analysis framework using Virtual Manufacturing techniques. Major components of the framework are identified and their functions are defined. Then, the framework is applied to the geometric tolerance analysis problem of precision machine tool spindle assemblies. As a result, a guideline of geometric tolerances for spindle design is suggested.