Manufacturing processes used in the production of biopharmaceutical or biological products should be evaluated for their ability to remove potential contaminants, including TSE agents. In the present study, we have evaluated scrapie prion protein (PrP Sc) removal in the presence of different starting materials, using virus removal filters of different pore sizes. Following 75 nm filtration, PrP Sc was detected in the filtrate by Western blot (WB) analysis when a "super-sonicated" microsomal fraction derived from hamster adapted scrapie strain 263K (263K MF) was used as the spike material. In contrast, no PrP Sc was detected when an untreated 263K MF was used. By using spike materials prepared in a manner designed to optimize the particle size distribution within the preparation, only 15 nm filtration was shown to remove PrP Sc to below the limits of detection of the WB assays used under all the experimental conditions. However, infectious PrP Sc was recovered following 15 nm filtration under one experimental condition. The results obtained suggest that the nature of the spike preparation is an important factor in evaluating the ability of filters to remove prions, and that procedures designed to minimize the particle size distribution of the prion spike, such as the "super-sonication" or detergent treatments described herein, should be used for the preparation of the spike materials.