A filter vial for separating biological and chemical fluids has a cylindrical sidewall with an open top and a closed bottom. A protrusion extends upwards from the middle of the bottom to form an annular recess. A tubular plunger has an open bottom end to which is fastened an annular cup having an outer sidewall sized to fit into and seal against the vial's sidewall. An inner sidewall of the annular cup holds a filter over an opening in the bottom of the plunger and forms a shaped cavity leading to that filter. The annular cup on the plunger fits into the annular recess in the vial to force fluid from the vial through the filter and into the plunger.