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For a wide variety of micromachined devices, designers need accurate analysis of fluid drag forces for complicated three-dimensional (3-D) problems. This paper describes FastStokes, a recently developed 3-D fluid analysis program. FastStokes rapidly computes drag forces on complicated structures by solving an integral formulation of the Stokes equation using a precorrected fast Fourier transform (PFFT)-accelerated boundary element method (BEM). The specializations of the PFFT algorithm to the Stokes flow problem are described, and computational results are presented. Timing results are used to demonstrate that FastStokes scales almost linearly with problem complexity, can easily analyze structures as complicated as an entire comb drive in under an hour, and can produce results that accurately match measured data.