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Shimming the flange of a vertical machine is primarily done to adjust the alignment of the machine components, particularly the shafts. When dealing with vertical machines, it's vital that the shafts are correctly aligned both in distance and angle to ensure efficient operation and to prevent excess wear or failure. The process of shimming specifically addresses the angular relationship between the shafts, allowing for precise adjustments to ensure proper engagement and functioning.

Shimming does not inherently change the distance between the shafts; rather, it focuses on optimizing the angle between them for better performance. This is crucial because improper alignment can lead to vibrations, increased energy consumption, and ultimately, mechanical failure.

In contrast, other options refer to aspects not directly related to the purpose of shimming. Adjusting clearance would pertain to gap management rather than angle alignment, lowering the center of gravity relates more to stability than alignment, and changing the distance between shafts is typically achieved through other means rather than shimming. Thus, shimming is fundamentally about fine-tuning alignment angles to achieve optimal machine performance.