A method filters particles from small volumes of fluid in a tubular vial having an open top and closed bottom with a tubular plunger sliding in the vial to force fluid through a filter at the end of the plunger and into a cavity in the plunger. The filter is held by a cap placed over the end of the plunger. The vial's bottom has an upward extending protrusion mating with a conforming recess in the cap to direct fluid to the protraction and filter as the cap abuts the bottom of the vial. Channels in the bottom help direct fluid flow.