The utilization of micro-scale technologies is limited by the speed of their manufacture. Micro-milling is one particular technology used to manufacture micro-scale parts which could benefit extensively from an increase in throughput. Micro-milling involves a rotating cutter slightly thicker than a human hair removing material while spinning at speeds often over one hundred thousand revolutions per minute. An obvious solution to the throughput bottleneck is to move current micro-mills faster using existing technology; however, simply increasing the operational speed of existing micro-mills will lead to vibration and trajectory following problems. If a micro-mill cannot be positioned precisely, then part tolerances cannot be maintained. Thus any increase in throughput would be counterproductive in terms of overall performance. This dissertation presents techniques to improve the performance of micro-mills, as well as other flexible machines. Theses improvements are possible through the utilization of the vibration suppression scheme of input shaping. By thoughtfully altering the commands sent to flexible systems, their vibration can be significantly reduced. Input shaping was effectively applied to an existing micro-mill, which improved part tolerances and increased operational speed. However, at extremely high speeds, traditional input shaping is not effective at following complicated trajectories. Therefore, new input shaping techniques were developed specifically for trajectory tracking of extremely fast motions on micro-mills and other flexible systems. Often machines cannot achieve these high speeds while maintaining their accuracy because of the mechanical design of the machines themselves. If the mechanical design of micro-mills and other machines consider flexible and lightweight design alternatives that utilize input shaping for vibration suppression instead of stiff and heavy designs, then faster machine motion will be possible. By considering input shaped flexible systems as part of traditional mechanical design processes, these flexible solutions allow vast performance improvement. Specifically, embodiment design can be improved through consideration of input shaping performance requirements. Through these advancements, this dissertation improves the design, control, and performance of micro-mills and other flexible machines.